Sequence assembly with MIRA3

The main one-stop-switches for most assemblies. You can choose between two different assembly methods (denovo or mapping), two different assembly types (genome or est), three different quality grades (draft, normal or accurate and mix different sequencing technologies (sanger, 454, solexa and solid). This switch is explained in more detail in the subsection "The --job= switch in detail".

A modifier switch for genome data that is deemed to be highly repetitive. The assemblies will run slower due to more iterative cycles that give mira a chance to resolve nasty repeats.

Switches off clipping options for given sequencing technologies. Technologies can be sanger, 454, solexa or solid. Multiple entries separated by comma.

Note that [-CL:pec] and the chimera clipping [-CL:ascdc] are not switched off by this parameter and should be switched off separately.

Examples:

Switches off loading TRACEINFO ancillary data in XML files for all technologies. Place it after [--fasta] and/or [--job=] quick switches.

Loads parameters from the filename given. Allows a maximum of 10 levels of recursion, i.e. a --params option appearing within a file that loads other parameter files (though I cannot think of useful applications with more than 3 levels).

Sets parameters suited for loading sequences from FASTA files. The version with =<filename> will also set the input file to the given filename.

Sets parameters suited for loading sequences from PHD files. The version with =<filename> will also set the input file to the given filename.

Sets parameters suited for loading sequences from CAF files. The version with =<filename> will also set the input file to the given filename.

Default is mira. Defines the project name for this assembly. The project name automatically influences the name of input and output files / directories. E.g. in the default setting, the file names for the output of the assembly in FASTA format would be mira_out.fasta and mira_out.fasta.qual. Setting the project name to "MyProject" would generate MyProject_out.fasta and MyProject_out.fasta.qual. See also -FILENAME: and -DIRECTORY: for a list of names that are influenced.

Default is mira. Works like [-project=<name>], but takes only effect on input files.

Default is mira. Works like [-project=<name>], but takes only effect on output files.

Same as the quick switch [-project]. Defines the name of your project and influences the naming of your input and output files.

Default is 2. Master switch to set the number of threads used in different parts of mira.

Note 1: currently only the SKIM algorithm uses multiple threads, other parts will follow.

Note 2: Although the main data structures are shared between the threads, there's some additional memory needed for each thread.

Note 3: when running the SKIM in parallel threads, MIRA can give different results when started with the same data and same arguments. While the effect could be averted for SKIM, the memory cost for doing so would be an additional 50% for one of the large tables, so this has not been implemented at the moment. Besides, at the latest when the Smith-Watermans run in parallel, this could not be easily avoided at all.

Default is Yes. Whether mira tries to optimise run time of certain algorithms in a space/time trade-off memory usage, increasing or reducing some internal tables as memory permits.

Note 1: This functionality currently relies on the /proc file system giving information on the system memory ("MemTotal" in /proc/meminfo) and the memory usage of the current process ("VmSize" in /proc/self/status). If this is not available, the functionality is switched off.

Note 2: The automatic memory management can only work if there actually is unused system memory. It's not a wonder switch which reduces memory consumption. In tight memory situations, memory management has no effect and the algorithms fall back to minimum table sizes. This means that the effective size in memory can grow larger than given in the memory management parameters, but then MIRA will try to keep the additional memory requirements to a minimum.

Default is 0. If automatic memory management is used (see above), this number is the size in gigabytes that the MIRA process will use as maximum target size when looking for space/time trade-offs. A value of 0 means that MIRA does not try keep a fixed upper limit.

Note: when in competition to [-GE:kpmf] (see below), the smaller of both sizes is taken as target. Example: if your machine has 64 GiB but you limit the use to 32 GiB, then the MIRA process will try to stay within these 32 GiB.

Default is 10. If automatic memory management is used (see above), this number works a bit like [-GE:mps] but the other way round: it tries to keep x percent of the memory free.

Note: when in competition to [-GE:mps] (see above), the argument leaving the most memory free is taken as target. Example: if your machine has 64 GiB and you limit the use to 42 GiB via [-GE:mps] but have a [-GE:kpmf] of 50, then the MIRA process will try to stay within 64-(64*50%)=32 GiB.

Default is 1. Controls the starting step of the SNP search in EST pipeline and is therefore only useful in miraSearchESTSNPs.

EST assembly is a three step process, each with different settings to the assembly engine, with the result of each step being saved to disk. If results of previous steps are present in a directory, one can easily "play around" with different setting for subsequent steps by reusing the results of the previous steps and directly starting with step two or three.

Default is Yes. Two reads sequenced from the same clone template form a read pair with a known minimum and maximum distance. This feature will definitively help for contigs containing lots of repeats. Set this to 'yes' if your data contains information on insert sizes (e.g. in paired-end sequencing).

Information on insert sizes can be given via the SI tag in EXP files (for each read pair individually), via insert_size and insert_stdev elements of NCBI TRACEINFO XML files or for the whole project using [-GE:tismin] and [-GE:tismax] (see below).

Additional information to set the orientation of the read-pairs can be given via [-GE:tpbd].

Default is -1. The default value for the minimum template size for reads that have no template size in ancillary data. If -1 is used as value, then no default value is given and reads without ancillary data giving this number will behave as if they had no template.

Default is -1. The default value for the maximum template size for reads that have no template size in ancillary data. If -1 is used as value, then no default value is given and reads without ancillary data giving this number will behave as if they had no template.

Default is -1 for all sequencing technologies.

This value tells MIRA how read-pairs of a template must be oriented in a contig to be valid. A value of "-1" means the orientation must be 5'-3' to 3'-5', a value of "1" means 5'-3' to 5'-3'.

Set this to "1" if you assemble paired-end 454 data downloaded from the Short Read Archives (SRAs, at the NCBI and EMBL). Set this also to "1" for Solexa data where the paired-end sequencing protocol used creates 5'-3' to 5'-3' pairs.

	Note
	Although with Solexa it is possible to build libraries in both directions, with MIRA it is currently not possible to mix within the same sequencing technology paired-end reads which need "-1" as direction with paired-end reads which have "1" as direction. This will be worked on if the need arises.

Default is yes. Controls whether date and time are printed out during the assembly. Suppressing it is not useful in normal operation, only when debugging or benchmarking.

Default is No. Defines whether to load data generated by a given technology.

Default is fasta. Takes effect only when [-LR:lsd]) is 'yes'.

Defines whether to load for assembly from FASTA sequences (<projectname>_in.fasta) and their qualities (<projectname>_in.fasta.qual), from a FASTQ file (<projectname>_in.fastq), from EXP files from a file of filenames (<projectname>_in.fofn), from a phd file (<projectname>_in.phd) or from a CAF file (<projectname>_in.caf) and assemble or eventually reassemble it.

Note 1: Only Sanger supports all file types. 454 and Solexa support only FASTA and FASTQ.

Note 2: fofnphd currently not available.

Default is SCF. Takes effect only when [-LR:lsd]) is 'yes' and for Sanger reads.

Defines the source format for reading qualities from external sources. Normally takes effect only when these are not present in the format of the load_job project (EXP and FASTA can have them, CAF and PHD must have them).

Takes effect only when [-LR:lsd]) is 'yes' and for Sanger reads.

Default is no, only takes effect when load_job is fofnexp. Defines whether or not the qualities from the external source override the possibly loaded qualities from the load_job project. This might be of use in case some post-processing software fiddles around with the quality values of the input file but one wants to have the original ones.

Default is yes. Takes effect only when [-LR:lsd]) is 'yes' and for Sanger reads.

Should there be a major mismatch between the external quality source and the sequence (e.g.: the base sequence read from a SCF file does not match the originally read base sequence), should the read be excluded from assembly or not. If not, it will use the qualities it had before trying to load the external qualities (either default qualities or the ones loaded from the original source).

Default is yes. When set to yes, MIRA will stop the assembly if there is no quality file for a given sequence file. E.g., if the FASTA quality file is missing when loading from FASTA.

Default is sanger for Sanger sequencing data, fr for 454 and solexa for Solexa. Defines the read naming scheme for read suffixes. These suffixes can be used by mira to deduce a template name if none is given in ancillary data.

Currently supported: Sanger centre, TIGR, simple forward / reverse naming, St. Louis schemes and Solexa/Illumina schemes are supported out of the box.

How to choose: please read the documentation available at the different centres or ask your sequence provider. In a nutshell (and probably over-simplified):

Default is no. This switch applies only for sequences from older Illumina / Solexa sequencing technology when loading from FASTA! Defines whether the FASTA quality file contains Solexa scores (which also have negative values) instead of quality values. Solexa scores also have negative values. If set to yes, mira will automatically convert the Solexa scores to phred style quality values.

Default is 0. This switch applies only for sequences loaded from FASTQ format!

Defines the quality offset used to convert characters into quality values. Usually, 33 is used for FASTQ in Sanger style, Solexa 1.0 format uses 59 (I think) and newer Solexa 1.3 format uses 64.

The default value of 0 switches on routines that try to guess the correct value from the data present in the FASTQ (which they do when the data contains at least one read which at least one base with quality between 0 and 4).

Default is no. Some file formats above (FASTA, PHD or even CAF and EXP) possibly do not contain all the info necessary or useful for each read of an assembly. Should additional information -- like clipping positions etc. -- be available in a XML trace info file in NCBI format (see File formats), then set this option to yes and it will be merged to all the data loaded, be it for Sanger, 454, Solexa or SOLiD technology. See also -FILENAME: for the name of the XML file to load.

Please note: quality clippings given here will override quality clippings loaded earlier (e.g. in EXP files) or performed by mira. Minimum clippings will still be made by the program, though.

Default is no. If set to yes, the project will not be assembled and no assembly output files will be produced. Instead, the project files will only be loaded. This switch is useful for checking consistency of input files.

Default is dependent of the sequencing technology and assembly quality level. Defines how many iterations of the whole assembly process are done.

Default is dependent of the sequencing technology and assembly quality level. Defines whether the skim algorithm (and with it also the recalculation of Smith-Waterman alignments) is called in-between each main pass. If set to no, skimming is done only when needed by the workflow: either when read extensions are searched for ( [-DP:ure]) or when possible vector leftovers are to be clipped ( [-CL:pvc]).

Setting this option to yes is highly recommended, setting it to no only for quick and dirty assemblies.

Default is dependent of the sequencing technology and assembly quality level. Defines the maximum number of times a contig can be rebuilt during a main assembly passes ([-AS:nop]) if misassemblies due to possible repeats are found.

Default is is currently yes. Tells mira to use coverage information accumulated over time to more accurately pinpoint reads that are in repetitive regions.

Default is 2.0 for all sequencing technologies in most assembly cases. This option says this: if mira a read has ever been aligned at positions where the total coverage of all reads of the same sequencing technology attained the average coverage times [-AS:ardct] (over a length of [-AS:ardml], see below), then this read is considered to be repetitive.

Default is dependent of the sequencing technology, currently 400 for Sanger and 200 for 454.

A coverage must be at least this number of bases higher than [-AS:ardct] before being really treated as repeat.

Default is dependent of the sequencing technology.

Default is currently yes for genome assemblies and no for EST assemblies or assemblies with Solexa data.

Takes effect only if uniform read distribution ([-AS:urd]) is on.

When set to yes, mira will analyse coverage of contigs built at a certain stage of the assembly and estimate an average expected coverage of reads for contigs. This value will be used in subsequent passes of the assembly to ensure that no part of the contig gets significantly more read coverage of reads that were previously identified as repetitive than the estimated average coverage allows for.

This switch is useful to disentangle repeats that are otherwise 100% identical and generally allows to build larger contigs. It is expected to be useful for Sanger and 454 sequences. Usage of this switch with Solexa data is currently not recommended.

It is a real improvement to disentangle repeats, but has the side-effect of creating some "contig debris" (small and low coverage contigs, things you normally can safely throw away as they are representing sequence that already has enough coverage).

This switch must be set to no for EST assembly, assembly of transcripts etc. It is recommended to also switch this off for mapping assemblies.

Default is dependent of the sequencing technology and assembly quality level. Recommended values are: 3 for an assembly with 3 to 4 passes ([-AS:nop]). Assemblies with 5 passes or more should set the value to the number of passes minus 2.

Takes effect only if uniform read distribution ([-AS:urd]) is on.

Default is 1.5 for all sequencing technologies in most assembly cases. The [--highlyrepetitive] quick-switch sets this to 1.2.

This option says this: if mira determined that the average coverage is $x$, then in subsequent passes it will allow coverage for reads determined to be repetitive to be built into the contig only up to a total coverage of $x*urdcm$. Reads that bring the coverage above the threshold will be rejected from that specific place in the contig (and either be built into another copy of the repeat somewhere else or end up as contig debris).

Please note that the lower [-AS:urdcm] is, the more contig debris you will end up with (contigs with an average coverage less than half of the expected coverage, mostly short contigs with just a couple of reads).

Takes effect only if uniform read distribution ([-AS:urd]) is on.

Default is is dependent on --job quality: currently no for draft and yes for normal and accurate. Switched of for EST assembly.

Tells mira to use keep repeats longer that the length of reads in separate contigs.

Default is dependent of the sequencing technology and assembly quality level. A spoiler can be either a chimeric read or it is a read with long parts of unclipped vector sequence still included (that was too long for the [-CL:pvc] vector leftover clipping routines). A spoiler typically prevents contigs to be joined, MIRA will cut them back so that they represent no more harm to the assembly.

Recommended for assemblies of mid- to high-coverage genomic assemblies, not recommended for assemblies of ESTs as one might loose splice variants with that.

A minimum number of two assembly passes ([-AS:nop]) must be run for this option to take effect.

Default is yes. Defines whether the spoiler detection algorithms are run only for the last pass or for all passes ( [-AS:nop]).

Takes effect only if spoiler detection ([-AS:sd]) is on. If in doubt, leave it to 'yes'.

Default is dependent of the sequencing technology. Defines the minimum length that reads must have to be considered for the assembly. Shorter sequences will be filtered out at the beginning of the process and won't be present in the final project.

Default is dependent of the sequencing technology and the [--job] parameter. For genome assemblies it's usually around 2 for Sanger, 5 for 454, 5 for PacBio and 10 for Solexa. In EST assemblies, it's currently 2 for all sequencing technologies.

Defines the minimum number of reads a contig must have before it is built or saved by MIRA. Overlap clusters with less reads than defined will not be assembled into contigs but reads in these clusters will be immediately transferred to debris.

This parameter is useful to considerably reduce assembly time in large projects with millions of reads (like in Solexa projects) where a lot of small "junk" contigs with contamination sequence or otherwise uninteresting data may be created otherwise.

	Note
	Note that a value larger 1 of this parameter interferes with the functioning of [-OUT:sssip] and [-OUT:stsip].

Default is currently 10 for all sequencing technologies. Defines the default base quality of reads that have no quality read from file.

Default is yes. When set to yes, MIRA will stop the assembly if any read has no quality values loaded.

Default is yes. MIRA has two different pathfinder algorithms it chooses from to find its way through the (more or less) complete set of possible sequence overlaps: a genomic and an EST pathfinder. The genomic looks a bit into the future of the assembly and tries to stay on safe grounds using a maximum of information already present in the contig that is being built. The EST version on the contrary will directly jump at the complex cases posed by very similar repetitive sequences and try to solve those first and is willing to fall back to first-come-first-served when really bad cases (like, e.g., coverage with thousands of sequences) are encountered.

Generally, the genomic pathfinder will also work quite well with EST sequences (but might get slowed down a lot in pathological cases), while the EST algorithm does not work so well on genomes. If in doubt, leave on yes for genome projects and set to no for EST projects.

Default is yes. Another important switch if you plan to assemble non-normalised EST libraries, where some ESTs may reach coverages of several hundreds or thousands of reads. This switch lets MIRA save a lot of computational time when aligning those extremely high coverage areas (but only there), at the expense of some accuracy.

Default is 500. Defines the number of potential partners a read must have for MIRA switching into emergency search stop mode for that read.

Default is no. Defines whether there is an upper limit of time to be used to build one contig. Set this to yes in EST assemblies where you think that extremely high coverages occur. Less useful for assembly of genomic sequences.

Default is 10000. Depending on [-AS:umcbt] above, this number defines the time in seconds allocated to building one contig.

Default is no. Straindata is a key value file, one read per line. First the name of the read, then the strain name of the organism the read comes from. It is used by the program to differentiate different types of SNPs appearing in organisms and classifying them.

Default is no for de-novo assemblies and yes for mapping.

Defines whether, after having loaded all data from all possible source, MIRA will assign a strain name to reads which didn't get strain information via said data files (either NCBI TRACEINFO XML files or the simple MIRA straindata files). The strain name to assign the is determined via [-SB:dsn] (see below).

Default is StrainX. Defines the strain name to assign to reads which don't have a strain name after loading, works only if [-SB:ads=yes] (see above).

Default is no. A backbone is a sequence (or a previous assembly) that is used as template for a mapping assembly. The current assembly process will assemble reads first to those loaded backbone contigs before creating new contigs (if any).

This feature is helpful for assembling against previous (and already possibly edited) assembly iterations, or to make a comparative assembly of two very closely related organisms. Please read "very closely related" as in: only SNP mutations or short indels present.

Default is dependent on assembly quality level chosen: 0 for 'draft', 1 for 'normal' and [-AS:nop] divided by 2 for 'accurate'.

When assembling against backbones, this parameter defines the pass iteration (see [-AS:nop]) from which on the backbones will be really used. In the passes preceding this number, the non-backbone reads will be assembled together as if no backbones existed. This allows mira to correctly spot repetitive stretches that differ by single bases and tag them accordingly. Note that full assemblies are considerably slower than mapping assemblies, so be careful with this when assembling millions of reads.

Rule of thumb: if backbones belong to same strain as reads to assemble, set to 1. If backbones are a different strain, then set [-SB:sbuib] to 1 lower than [-AS:nop] (example: nop=4 and sbuip=3).

Default isReferenceStrain. Defines the name of the strain that the backbone sequences have.

Default is no. Useful when using CAF as input for backbone: forces all reads of the backbone contigs to get assigned the new backbone strain, even if they previously had other strains assigned.

Main usage is in multi-step hybrid assemblies.

Default is Default is an empty string. Useful when using CAF as input for backbone: when set to a given strain name, mira will internally use only reads from the given strain to build the rails it will use to align reads.

Main usage is in multi-step hybrid assemblies.

Default is fasta. Defines the filetype of the backbone file given. Currently only FASTA, CAF and GBF files are supported.

When GBF (GenBank files, more commonly named '.gbk') files are loaded, the features within theses files are automatically transformed into Staden compatible tags and get passed through the assembly.

Default is 0. Parameter for the internal sectioning size of the backbone to compute optimal alignments. Should be set to two times length of longest read in input data + 15%. When set to 0, MIRA will compute optimal values from the data loaded.

Default is 0. Parameter for the internal sectioning size of the backbone to compute optimal alignments. Should be set to length of the longest read. When set to 0, MIRA will compute optimal values from the data loaded.

Default is -1. Defines the default quality that the backbone sequences have if they came without quality values in their files (like in GBF format or when FASTA is used without .qual files). A value of -1 mira to use the same default quality for backbones as for reads.

Default is no. Standard mapping assembly mode of the assembler is to map available reads to a backbone and discard reads that do not fit. If set to 'yes', mira will use reads that did not map to the backbone(s) to make new contigs (if possible). Please note: while a simple mapping assembly is comparatively cheap in terms of memory and time consumed, setting this option to 'yes' means that behind the scenes data for a full blown de-novo assembly is generated in addition to the data needed for a mapping assembly, which makes it a bit more costly that a de-novo assembly per se.

Default is dependent of the sequencing technology used: yes for Sanger, no for all others. mira expects the sequences it is given to be quality clipped. During the assembly though, it will try to extend reads into the clipped region and gain additional coverage by analysing Smith-Waterman alignments between reads that were found to be valid. Only the right clip is extended though, the left clip (most of the time containing sequencing vector) is never touched.

Default is dependent of the sequencing technology used. Only takes effect when [-DP:ure] (see above) is set to yes. The read extension routines use a sliding window approach on Smith-Waterman alignments. This parameter defines the window length.

Default is dependent of the sequencing technology used. Only takes effect when [-DP:ure] (see above) is set to yes. The read extension routines use a sliding window approach on Smith-Waterman alignments. This parameter defines the number maximum number of errors (=disagreements) between two alignment in the given window.

Default is dependent of the sequencing technology used. Only takes effect when [-DP:ure] (see above) is set to yes. The read extension routines can be called before assembly and/or after each assembly pass (see [-AS:nop]). This parameter defines the first pass in which the read extension routines are called. The default of 0 tells mira to extend the reads the first time before the first assembly pass.

Default is dependent of the sequencing technology used. Only takes effect when [-DP:ure] (see above) is set to yes. The read extension routines can be called before assembly and/or after each assembly pass (see [-AS:nop]). This parameter defines the last pass in which the read extension routines are called. The default of 0 tells mira to extend the reads the last time before the first assembly pass.

Default is no. Uses the parameters [-CL:msvsgs:msvsmfg:msvsmeg] (see below).

Before running mira, the ssaha2 or smalt programs from the Sanger centre can be used to detect possible vector sequence stretches in the input data for the assembly. This parameter - if set to yes - will let mira load the result file of a ssaha2 or smalt run and tag the possible vector sequences at the ends of reads.

ssaha2 must be called like this "ssaha2 <ssaha2options> vector.fasta sequences.fasta" to generate an output that can be parsed by mira. In the above example, replace vector.fasta by the name of the file with your vector sequences and sequences.fasta by the name of the file containing your sequencing data.

smalt must be called like this: "smalt map -f ssaha <ssaha2options> hash_index sequences.fasta

This makes you basically independent from any other commercial or license-requiring vector screening software. For Sanger reads, a combination of lucy and ssaha2 or smalt together with this parameter should do the trick. For reads coming from 454 pyro-sequencing, ssaha2 or smalt and this parameter will also work very well. See the usage manual for a walkthrough example on how to use SSAHA2 / SMALT screening data.

Note 1: the output format of SSAHA2 must the native output format (-output ssaha2). For SMALT, the output option -f ssaha must be used. Other formats cannot be parsed by MIRA.

Note 2: when using SSAHA2 results, the input file must be named <projectname>_ssaha2vectorscreen_in.txt. When using SMALT results, the input file must be named <projectname>_smaltvectorscreen_in.txt.

Note 3: if both a ssah2 and smalt result file are present, both will be read.

Note 4: I currently use the following SSAHA2 options: -kmer 8 -skip 1 -seeds 1 -score 12 -cmatch 9 -ckmer 6

Note 5: Anyone contributing SMALT parameters?

Note 6: the sequence vector clippings generated from SSAHA2 / SMALT data do not replace sequence vector clippings loaded via the EXP, CAF or XML files, they rather extend them.

Default is dependent of the sequencing technology used. Takes effect only if [-CL:msvs] is yes. While performing the clip of screened vector sequences, mira will look if it can merge larger chunks of sequencing vector bases that are a maximum of [-CL:msvgsgs] apart.

Default is dependent of the sequencing technology used. Takes effect only if [-CL:msvs] is yes. While performing the clip of screened vector sequences at the start of a sequence, mira will allow up to this number of non-vector bases in front of a vector stretch.

Default is dependent of the sequencing technology used. Takes effect only if [-CL:msvs] is yes. While performing the clip of screened vector sequences at the end of a sequence, mira will allow up to this number of non-vector bases behind a vector stretch.

Default is dependent of the sequencing technology used: yes for Sanger, no for any other. mira will try to identify possible sequencing vector relics present at the start of a sequence and clip them away. These relics are usually a few bases long and were not correctly removed from the sequence in data preprocessing steps of external programs.

You might want to turn off this option if you know (or think) that your data contains a lot of repeats and the option below to fine tune the clipping behaviour does not give the expected results.

You certainly want to turn off this option in EST assemblies as this will quite certainly cut back (and thus hide) different splice variants. But then make certain that you pre-processing of Sanger data (sequencing vector removal) is good, other sequencing technologies are not affected then.

Default is dependent of the sequencing technology used. The clipping of possible vector relics option works quite well. Unfortunately, especially the bounds of repeats or differences in EST splice variants sometimes show the same alignment behaviour than possible sequencing vector relics and could therefore also be clipped.

To refrain the vector clipping from mistakenly clip repetitive regions or EST splice variants, this option puts an upper bound to the number of bases a potential clip is allowed to have. If the number of bases is below or equal to this threshold, the bases are clipped. If the number of bases exceeds the threshold, the clip is NOT performed.

Setting the value to 0 turns off the threshold, i.e., clips are then always performed if a potential vector was found.

Default is no. This will let mira perform its own quality clipping before sequences are entered into the assembly. The clip function performed is a sequence end window quality clip with back iteration to get a maximum number of bases as useful sequence. Note that the bases clipped away here can still be used afterwards if there is enough evidence supporting their correctness when the option [-DP:ure] is turned on.

Warning: The windowing algorithm works pretty well for Sanger, but apparently does not like 454 type data. It's advisable to not switch it on for 454. Beside, the 454 quality clipping algorithm performs a pretty decent albeit not perfect job, so for genomic 454 data (not! ESTs), it is currently recommended to use a combination of [-CL:emrc] and [-DP:ure].

Default is dependent of the sequencing technology used. This is the minimum quality bases in a window require to be accepted. Please be cautious not to take too extreme values here, because then the clipping will be too lax or too harsh. Values below 15 and higher than 30-35 are not recommended.

Default is dependent of the sequencing technology used. This is the length of a window in bases for the quality clip.

Default is no. This option allows to clip reads that were not correctly preprocess and have unclipped bad quality stretches that might prevent a good assembly.

mira will search the sequence in forward direction for a stretch of bases that have in average a quality less than a defined threshold and then set the right quality clip of this sequence to cover the given stretch.

Default is dependent of the sequencing technology used. Defines the minimum average quality a given window of bases must have. If this quality is not reached, the sequence will be clipped at this position.

Default is dependent of the sequencing technology used. Defines the length of the window within which the average quality of the bases are computed.

Default is dependent of the sequencing technology used. This will let mira perform a 'clipping' of bases that were masked out (replaced with the character X). It is generally not a good idea to use mask bases to remove unwanted portions of a sequence, the EXP file format and the NCBI traceinfo format have excellent possibilities to circumvent this. But because a lot of preprocessing software are built around cross_match, scylla- and phrap-style of base masking, the need arose for mira to be able to handle this, too. mira will look at the start and end of each sequence to see whether there are masked bases that should be 'clipped'.

Default is dependent of the sequencing technology used. While performing the clip of masked bases, mira will look if it can merge larger chunks of masked bases that are a maximum of [-CL:mbcgs] apart.

Default is dependent of the sequencing technology used. While performing the clip of masked bases at the start of a sequence, mira will allow up to this number of unmasked bases in front of a masked stretch.

Default is dependent of the sequencing technology used. While performing the clip of masked bases at the end of a sequence, mira will allow up to this number of unmasked bases behind a masked stretch.

Default is dependent of the sequencing technology used: on for 454 data, off for all others. This will let mira perform a 'clipping' of bases that are in lowercase at both ends of a sequence, leaving only the uppercase sequence. Useful when handling 454 data that does not have ancillary data in XML format.

Default is no. This option is useful in EST assembly. Poly-A stretches in forward reads and poly-T stretches in reverse reads that were not correctly masked or clipped in preprocessing steps from external programs get clipped or tagged here. The assembler will not use these stretches for critical operations.

Default is no. This option is currently not active (as of version 2.9.22).

In future, this will allow to keep the poly-A signal in the reads and tag them. The tags provide a good visual anchor when looking at the assembly with different programs.

Default is 10. Only takes effect when [-CP:cpat] (see above) is set to yes. Defines the number of ``A'' (in forward direction) or ``T'' (in reverse direction'' must be present to be considered a poly-A signal stretch.

Default is 1. Only takes effect when [-CL:cpat] (see above) is set to yes. Defines the maximum number of errors allowed in the potential poly-A signal stretch. The distribution of these errors is not important.

Default is 9. Only takes effect when [-CL:cpat] (see above) is set to yes.Defines the number of bases from the end of a sequence (if masked: from the end of the masked area) within which a poly-A signal stretch is looked for.

Default is dependent of the sequencing technology used. If on, ensures a minimum left clip on each read according to the parameters in [-CL:mlcr:smlc]

Default is dependent of the sequencing technology used. If [-CL:emlc] is on, checks whether there is a left clip which length is at least the one specified here.

Default is dependent of the sequencing technology used. If [-CL:emlc] is on and actual left clip is < [-CL:mlcr], set left clip of read to the value given here.

Default is dependent of the sequencing technology used. If on, ensures a minimum right clip on each read according to the parameters in [-CL:mrcr:smrc]

Default is dependent of the sequencing technology used. If [-CL:emrc] is on, checks whether there is a right clip which length is at least the one specified here.

Default is dependent of the sequencing technology used. If [-CL:emrc] is on and actual right clip is < [-CL:mrcr], set the length of the right clip of read to the value given here.

Default is yes for [--job=genome] assemblies and no for [--job=est] assemblies.

The SKIM routines of MIRA can be also used without much time overhead to find chimeric reads. When this parameter is set, MIRA will use that info to cut back chimeras to their longest non-chimeric length.

	Warning
	When working on low coverage data (e.g. < 5 to 6x Sanger and < 10x 454, you may want to switch off this option if you try to go for the longest contigs. Reason: single reads joining otherwise disjunct contigs will probably be categorised as chimeras.

Default is currently no.

The SKIM routines of MIRA can be also used without much time overhead to find junk sequence at end of reads. When this parameter is set, MIRA will use that info to cut back junk in reads.

It is currently suggested to leave this parameter switched off as the routines seem to be a bit too "trigger happy" and also cut back perfectly valid sequences.

Default is is dependent on --job quality: currently no for draft and yes for normal and accurate. Switched off for EST assembly.

This implements a pretty powerful strategy to ensure a good "high confidence region" (HCR) in reads, basically eliminating 99.9% of all junk at the 5' and 3' ends of reads. Note that one still must ensure that sequencing vectors (Sanger) or adaptor sequences (454) are "more or less" clipped prior to assembly.

	Warning
	Extremely effective, but should NOT be used for very low coverage genomic data, for EST projects or if one wants to retain rare transcripts.

Default is is dependent yes.

Solexa data has a pretty awful problem with in some reads when a GGCxG motif occurs (read more about it in the chapter on Solexa data). In short: the sequencing errors produced by this problem lead to many false positive SNP discoveries in mapping assemblies or problems in contig building in de-novo assembly.

MIRA knows about this problem and can look for it in Solexa reads during the proposed end clipping and further clip back the reads, greatly minimising the impact of this problem.

Default is is dependent on --job: currently 17 for Sanger and 454, 21 for Solexa.

This parameter defines the minimum number of bases at each end of a read that should be free of any sequencing errors. Note that the algorithm is based on SKIM hashing (see below), and compares hashes of all reads with each other. Therefore, using values less than 12 will lead to false negative hits.

Number of threads used in SKIM, default is 2. A few parts of SKIM are non-threaded, so the speedup is not exactly linear, but it should be very close. E.g., with 2 processors I get a speedup of 180-195%, with 4 between 350 and 395%.

Although the main data structures are shared between the threads, there's some additional memory needed for each thread.

Default is on. Defines whether SKIM searches for matches only in forward/forward direction or whether it also looks for forward/reverse direction.

You usually will not want to touch the default, except for very special application cases where you do not want MIRA to use reverse complement sequences at all.

If only Sanger or 454 data is used, default is 14 on 32 bit systems and 16 on 64 bit systems. Controls the number of consecutive bases $n$ which are used as a word hash. The higher the value, the faster the search. The lower the value, the more weak matches are found. Values below 10 are not recommended.

Default is 4. This is a parameter controlling the stepping increment $s$ with which hashes are generated. This allows for a more fine grained search as matches are found with at least $n+s$ (see [-SK:bph]) equal bases. The higher the value, the faster the search. The lower the value, the more weak matches are found.

Default is dependent of the sequencing technology used and assembly quality wished. Controls the relative percentage of exact word matches in an approximate overlap that has to be reached to accept this overlap as possible match. Increasing this number will decrease the number of possible alignments that have to be checked by Smith-Waterman later on in the assembly, but it also might lead to the rejection of weaker overlaps (i.e. overlaps that contain a higher number of mismatches).

Note: most of the time it makes sense to keep this parameter in sync with [-AL:mrs].

Default is 2000. Controls the maximum number of possible hits one read can maximally transport to the graph edge reduction phase. If more potential hits are found, only the best ones are taken.

In the pre-2.9.x series, this was an important option for tackling projects which contain extreme assembly conditions. It still is if you run out of memory in the graph edge reduction phase. Try then to lower it to 1000, 500 or even 100.

As the assembly increases in passes ([-AS:nop]), different combinations of possible hits will be checked, always the probably best ones first. So the accuracy of the assembly should only suffer when lowering this number too much.

During SKIM analysism, MIRA will estimate how repetitive parts of reads are. Parts which are occuring less than [-SK:fenn] times the average occurence will be tagged with a HAF2 (less than average) tag.

During SKIM analysism, MIRA will estimate how repetitive parts of reads are. Parts which are occuring more than [-SK:fenn] but less than [-SK:fexn] times the average occurence will be tagged with a HAF3 (normal) tag.

During SKIM analysism, MIRA will estimate how repetitive parts of reads are. Parts which are occuring more than [-SK:fexn] but less than [-SK:fer] times the average occurence will be tagged with a HAF4 (above average) tag.

During SKIM analysism, MIRA will estimate how repetitive parts of reads are. Parts which are occuring more than [-SK:fer] but less than [-SK:fehr] times the average occurence will be tagged with a HAF5 (repeat) tag.

During SKIM analysism, MIRA will estimate how repetitive parts of reads are. Parts which are occuring more than [-SK:fehr] but less than [-SK:fecr] times the average occurence will be tagged with a HAF6 (heavy repeat) tag. Parts which are occuring more than [-SK:fecr] but less than [-SK:nrr] times the average occurence will be tagged with a HAF7 (crazy repeat) tag.

Default is dependent on --job type: yes for de-novo, no for mapping. Tells mira to mask during the SKIM phase subsequences of size [-SK:nph] nucleotides that appear more often than the median occurrence of subsequences would otherwise suggest. The threshold from which on subsequences are considered nasty is set by [-SK:nrr] (see below).

There's one drawback though: the smaller the reads are that you try to assemble with this option turned on, the higher the probability that your reads will not span nasty repeats completely, therefore leading to a abortion of contig building at this site.

The masked parts are tagged with "MNRr" in the reads.

This option is extremely useful for assembly of larger projects (fungi-size) with a high percentage of repeats. Or in non-normalised EST projects, to get at least something assenbled.

Although it is expected that bacteria will not really need this, leaving it turned on will probably not harm except in unusual cases like several copies of (pro-)phages integrated in a genome.

Default is depending on the [--job=...] parameters. Normally it's high (around 100) for genome assemblies, but much lower (20 or less) for EST assemblies.

Sets the ratio from which on subsequences are considered nasty and hidden from the SKIM overlapper with a MNRr tag. The value of 10 means: mask all k-mers of [-SK:bph] length which are occurring more than 10 times more often than the average of the project.

Default is 6. Sets the minimum level of the HAF tags from which on MIRA will report tentatively repetitive sequence in the *_info_readrepeats.lst file of the info directory.

A value of 0 means "switched off". The default value of , 6 means all subsequences tagged with HAF6, HAF7 and MNRr will be logged. If you, e.g., only wanted MNRr logged, you'd use 8 as parameter value.

See also [-SK:fenn:fexn:fer:fehr:mnr:nrr] to set the different levels for the HAF and MNRr tags.

Default is 0. If the number of reads identified as megahubs exceeds the allowed ratio, mira will abort.

This is a fail-safe parameter to avoid assemblies where things look fishy. In case you see this, you might want to ask for advice on the mira_talk mailing list. In short: bacteria should never have megahubs (90% of all cases reported were contamination of some sort and the 10% were due to incredibly high coverage numbers). Eukaryotes are likely to contain megahubs if filtering is [-SK:mnr] not on.

EST project however, especially from non-normalised libraries, will very probably contain megahubs. In this case, you might want to think about masking, see [-SK:mnr].

Default is 15000000. Has no influence on the quality of the assembly, only on the maximum memory size needed during the skimming. The default value is equivalent to approximately 500MB.

Note: reducing the number will increase the run time, the more drastically the bigger the reduction. On the other hand, increasing the default value chosen will not result in speed improvements that are really noticeable. In short: leave this number alone if you are not desperate to save a few MB.

Default is 1024, 2048 when Solexa sequences are used. Maximum memory used (in MiB) during the reduction of skim hits.

Note: has no influence on the quality of the assembly, reducing the number will increase the runtime, the more drastically the bigger the reduction as hits then must be streamed multiple times from disk.

The default is good enough for assembly of bacterial genomes or small eukaryotes (using Sanger and/or 454 sequences). As soon as assembling something bigger than 20 megabases, you should increase it to 2048 or 4096 (equivalent to 2 or 4 GiB of memory).

Default is dependent of the sequencing technology used. The banded Smith-Waterman alignment uses this percentage number to compute the bandwidth it has to use when computing the alignment matrix. E.g., expected overlap is 150 bases, bip=10 -> the banded SW will compute a band of 15 bases to each side of the expected alignment diagonal, thus allowing up to 15 unbalanced inserts / deletes in the alignment. INCREASING AND DECREASING THIS NUMBER: increase: will find more non-optimal alignments, but will also increase SW runtime between linear and \Circum2. decrease: the other way round, might miss a few bad alignments but gaining speed.

Default is dependent of the sequencing technology used. Minimum bandwidth in bases to each side.

Default is dependent of the sequencing technology used. Maximum bandwidth in bases to each side.

Default is dependent of the sequencing technology used. Minimum number of overlapping bases needed in an alignment of two sequences to be accepted.

Default is dependent of the sequencing technology used. Describes the minimum score of an overlap to be taken into account for assembly. mira uses a default scoring scheme for SW align: each match counts 1, a match with an N counts 0, each mismatch with a non-N base -1 and each gap -2. Take a bigger score to weed out a number of chance matches, a lower score to perhaps find the single (short) alignment that might join two contigs together (at the expense of computing time and memory).

Default is dependent of the sequencing technology used. Describes the min % of matching between two reads to be considered for assembly. Increasing this number will save memory, but one might loose possible alignments. I propose a maximum of 80 here. Decreasing below 55% will make memory and time consumption probably explode.

Note: most of the time it makes sense to keep this parameter in sync with [-SK:pr].

Default is dependent of the sequencing technology used. Defines whether or not to increase penalties applied to alignments containing long gaps. Setting this to 'yes' might help in projects with frequent repeats. On the other hand, it is definitively disturbing when assembling very long reads containing multiple long indels in the called base sequence ... although this should not happen in the first place and is a sure sign for problems lying ahead.

When in doubt, set it to yes for EST projects and de-novo genome assembly, set it to no for assembly of closely related strains (assembly against a backbone).

When set to no, it is recommended to have [-CO:amgb] and [-CO:amgbemc] both set to yes.

Default is dependent of the sequencing technology used. Has no effect if extra_gap_penalty is off. Defines an extra penalty applied to 'long' gaps. There are these are predefined levels: low - use this if you expect your base caller frequently misses 2 or more bases. medium - use this if your base caller is expected to frequently miss 1 to 2 bases. high - use this if your base caller does not frequently miss more than 1 base.

For some stages of the EST assembly process, a special value split_on_codongaps is used. It's even a tick harsher that the 'high' level.

Also, usage of this parameter is probably a good thing if the repeat marker of the contig is set to not mark on gap bases ([-CO:amgb] equals to no). This is generally the case for 454 data.

Default is 100. Has no effect if extra_gap_penalty is off. Defines the maximum extra penalty in percent applied to 'long' gaps.

Default is <projectname>. Contigs will have this string prepended to their names. The [-project=] quick-switch will also change this option.

Default is dependent of the sequencing technology used. When adding reads to a contig, reject the reads if the drop in the quality of the consensus is > the given value in %. Lower values mean stricter checking. This value is doubled should a read be entered that has a template partner (a read pair) at the right distance.

Default is yes. One of the most important switches in MIRA: if set to yes, MIRA will try to resolve misassemblies due to repeats by identifying single base stretch differences and tag those critical bases as RMB (Repeat Marker Base, weak or strong). This switch is also needed when MIRA is run in EST mode to identify possible inter-, intra- and intra-and-interorganism SNPs.

Default is no. Only takes effect when [-CO:mr] (see above) is set to yes. If set to yes, MIRA will not use the repeat resolving algorithm during build time (and therefore will not be able to take advantage of this), but only before saving results to disk.

This switch is useful in some (rare) cases of mapping assembly.

Default is no. Only takes effect when [-CO:mr] (see above) is set to yes, effect is also dependent on the fact whether strain data (see - [-SB:lsd]) is present or not. Usually, mira will mark bases that differentiate between repeats when a conflict occurs between reads that belong to one strain. If the conflict occurs between reads belonging to different strains, they are marked as SNP. However, if this switch is set to yes, conflict within a strain are also marked as SNP.

This switch is mainly used in assemblies of ESTs, it should not be set for genomic assembly.

Default is dependent of the sequencing technology used. Only takes effect when [-CO:mr] (see above) is set to yes. This defines the minimum number of reads in a group that are needed for the RMB (Repeat Marker Bases) or SNP detection routines to be triggered. A group is defined by the reads carrying the same nucleotide for a given position, i.e., an assembly with mrpg=2 will need at least two times two reads with the same nucleotide (having at least a quality as defined in [-CO:mgqrt]) to be recognised as repeat marker or a SNP. Setting this to a low number increases sensitivity, but might produce a few false positives, resulting in reads being thrown out of contigs because of falsely identified possible repeat markers (or wrongly recognised as SNP).

Default is dependent of the sequencing technology used. Takes only effect when [-CO:mr] is set to yes. This defines the minimum quality of neighbouring bases that a base must have for being taken into consideration during the decision whether column base mismatches are relevant or not.

Default is dependent of the sequencing technology used. Takes only effect when [-CO:mr] is set to yes. This defines the minimum quality of a group of bases to be taken into account as potential repeat marker. The lower the number, the more sensitive you get, but lowering below 25 is not recommended as a lot of wrongly called bases can have a quality approaching this value and you'd end up with a lot of false positives. The higher the overall coverage of your project, the better, and the higher you can set this number. A value of 35 will probably remove most false positives, a value of 40 will probably never show false positives ... but will generate a sizable number of false negatives.

Default is dependent of the sequencing technology used. Takes only effect when [-CO:mr] is set to yes. Using the end of sequences of Sanger type shotgun sequencing is always a bit risky, as wrongly called bases tend to crowd there or some sequencing vector relics hang around. It is even more risky to use these stretches for detecting possible repeats, so one can define an exclusion area where the bases are not used when determining whether a mismatch is due to repeats or not.

Default is yes. When [-CL:pec] is set, the end-read exclusion area can be considerably reduced. Setting this parameter will automatically do this.

	Note
	Although the parameter is named "set to 1", it may be that the exclusion area is actually a bit larger (2 to 4), depending on what users will report back as "best" option.

Default is dependent of the sequencing technology used. Determines whether columns containing gap bases (indels) are also tagged.

Note: it is strongly recommended to not set this to 'yes' for 454 type data.

Default is yes. Takes effect only when [-CO:amgb] is set to yes. Determines whether multiple columns containing gap bases (indels) are also tagged.

Default is yes. Takes effect only when [-CO:amgb] is set to yes. Determines whether both for tagging columns containing gap bases, both strands.need to have a gap. Setting this to no is not recommended except when working in desperately low coverage situations.

Default is no for all sequencing types. If set to yes, mira will be forced to make a choice for a consensus base (A,C,G,T or gap) even in unclear cases where it would normally put a IUPAC base. All other things being equal (like quality of the possible consensus base and other things), mira will choose a base by either looking for a majority vote or, if that also is not clear, by preferring gaps over T over G over C over finally A.

mira makes a considerable effort to deduce the right base at each position of an assembly. Only when cases begin to be borderline it will use a IUPAC code to make you aware of potential problems. It is suggested to leave this option to no as IUPAC bases in the consensus are a sign that - if you need 100% reliability - you really should have a look at this particular place to resolve potential problems. You might want to set this parameter to yes in the following cases: 1) when your tools that use assembly result cannot handle IUPAC bases and you don't care about being absolutely perfect in your data (by looking over them manually). 2) when you assemble data without any quality values (which you should not do anyway), then this method will allow you to get a result without IUPAC bases that is "good enough" with respect to the fact that you did not have quality values.

Important note: in case you are working with a hybrid assembly, mira will still use IUPAC bases at places where reads from different sequencing types contradict each other. In fact, when not forcing non-IUPAC bases for hybrid assemblies, the overall consensus will be better and probably have less IUPAC bases as mira can make a better use of available information.

Default is yes for all Solexas when in a mapping assembly, else it's no. Can only be used in mapping assemblies. If set to yes, mira will merge all perfectly mapping Solexa reads into longer reads while keeping quality and coverage information intact.

This features hugely reduces the number of Solexa reads and makes assembly results with Solexa data small enough to be handled by current finishing programs (gap4, consed, others) on normal workstations.

Default is no. Once contigs have been build, mira can call a built-in versions of the automatic contig editors. For Sanger reads this is EdIt, for 454 reads it is a specially crafted editor that knows about deficiencies of the 454 technology (homopolymers).

EdIt will try to resolve discrepancies in the contig by performing trace analysis and correct even hard to resolve errors. This option is always useful, but especially in conjunction with [-AS:nop] and [-DP:ure] (see above).

Notice 1: the current development version has a memory leak in the editor, therefore the option is not automatically turned on.

Notice 2: it is strongly suggested to turn this option on for 454 data as this greatly improves the quality.

Default is yes. Only for Sanger data. If set to yes, the automatic editor will not take error hypotheses with a low probability into account, even if all the requirements to make an edit are fulfilled.

Default is 50. Only for Sanger data. The higher this value, the more strict the automatic editor will apply its internal rule set. Going below 40 is not recommended.

Default is yes. MIRA will check whether the log directory is running on an NFS mount. If it is and [-MI:sonfs] is active, MIRA will stop with a warning message.

	Warning
	You should never ever at all run MIRA on a NFS mounted directory ... or face the the fact that the assembly process may very well take 10 times longer (or more) than normal. You have been warned.

Default is 500. This parameter has absolutely no influence whatsoever on the assembly process of MIRA. But is used in the reporting within the *_assembly_info.txt file after the assembly where MIRA reports statistics on large and all contigs. [-MI:lcs] is the threshold value for categorising contigs.

Default is 5000 for [--job=genome] and 1000 for [--job=est].

This parameter is used for internal statistics calculations and has a subtle influence when being in a [--job=genome] assembly mode.

MIRA uses coverage information of an assembly project to find out about potentially repetitive areas in reads (and thus, a genome). To calculate statistics which are reflecting the approximate truth, the value of [-MI:lcs4s] is used as a cutoff threshold: contigs smaller than this value do not contribute to the calculation of average coverage while contigs larger or equal to this value do. Having this cutoff discards small contigs which tend to muddy the picture of avergae coverage of a project.

If in doubt, don't touch this parameter.

Default is an empty string. When set to a non-empty string, MIRA will create the log directory at the given location instead of using the current working directory.

This option is particularly useful for systems which have solid state disks (SSDs) which can be used for temporary files. Or in projects where the input and output files reside on a NFS mounted directory (current working dir), to put the log directory somewhere outside the NFS (see also: Things you should not do).

In both cases above, and for larger projects, MIRA then runs a lot faster.

Default is gap4da. Defines the extension of the directory where mira will write the result of an assembly ready to import into the Staden package (GAP4) in Direct Assembly format. The name of the directory will then be <projectname>_.<extension>

Default is .. Defines the directory where mira should search for experiment files (EXP).

Default is .. Defines the directory where mira should search for SCF files.

Default is <projectname>_in.<seqtype>.fasta. Defines the fasta file to load sequences of a project from.

Default is <projectname>_in.<seqtype>.fasta.qual. Defines the file containing base qualities. Although the order of reads in the quality file does not need to be the same as in the fasta or fofn (although it saves a bit of time if they are).

Default is <projectname>_in.<seqtype>.fastq. Defines the fastq file to load sequences of a project from.

Default is <projectname>_in.<seqtype>.caf. Defines the file to load a CAF project from. Filename must end with '.caf'.

Default is <projectname>_in.fofn. Defines the file of filenames where the names of the EXP files of a project are located.

Default is <projectname>_in.fofn. Defines the file of filenames where the names of the PHD files of a project are located. Note: this is currently not available.

Default is <projectname>_in.phd. Defines the file of where all the sequences of a project are in PHD format.

Default is <projectname>_straindata_in.txt. Defines the file to load straindata from..

Default is <projectname>_xmltraceinfo_in.<seqtype>.xml. Defines the file to load a trace info file in XML format from. This can be used both when merging XML data to loaded files or when loading a project from an XML trace info file.

Default is <projectname>_ssaha2vectorscreen_in.txt. Defines the file to load a the info about possible vector sequence stretches.

Default is <projectname>_smaltvectorscreen_in.txt. Defines the file to load a the info about possible vector sequence stretches.

Default is <projectname>_in.<seqtype>.<filetype>. Defines the file to load a backbone from. Note that you still must define the file type with [-SB:bft].

Default is no. Controls whether 'unimportant' singlets are written to the result files.

	Note
	Note that a value larger 1 of the [-AS:mrpc] parameter will disable the function of this parameter.

Default is yes. Controls whether singlets which have certain tags (see below) are written to the result files, even if [-OUT:sssip] (see above) is set.

If one of the (SRMr, CRMr, WRMr, SROr, SAOr, SIOr) tags appears in a singlet, MIRA will see that the singlets had been part of a larger alignment in earlier passes and even was part of a potentially 'important' decision. To give the possibility to human finishers to trace back the decision, these singlets can be written to result files.

	Note
	Note that a value larger 1 of the [-AS:mrpc] parameter will disable the function of this parameter.

Default is yes. Removes log files once they should not be needed anymore during the assembly process.

Default is no. Removes the complete log directory at the end of the assembly process. Some logs contain useful information that you may want to analyse though.

Default is yes.

Default is yes.

Default is yes for projects only with Sanger reads, 'no' as soon as there are 454, Solexa or SOLiD reads involved.

	Note
	MIRA will automatically switch to no (and cannot be forced to 'yes') when 454 or Solexa reads are present in the project as this ensure that the file system does not get flooded with millions of files.

Default is yes.

Default is yes.

Note

The ACE output of MIRA is conforming to the file specification given in the consed documentation. However, due to a bug in consed, consed cannot correctly load tags set by MIRA. There is a workaround: the MIRA distribution comes with a small Tcl script fixACE4consed.tcl which implements a workaround to allow consed loading the ACE generated by MIRA. Use the script like this: $ fixACE4consed.tcl infile.ace >outfile.ace and then load the resulting outfile into consed.

Default is no.

Default is yes.

Default is no.

Default is no.

Default is no.

Default is no.

Default is no.

Default is no.

Default is no.

Default is no.

Default is no.

Default is no.

Default is no.

Default is no.

Default is no.

Default is no.

Default is no.

Default is 60. When producing an output in text format ( [-OUT:ort|ott|oett]), this parameter defines how many bases each line of an alignment should contain.

Default is 60. When producing an output in HTML format, ( [-OUT:orh|oth|oeth]), this parameter defines how many bases each line of an alignment should contain.

Default is (a blank). When producing an output in text format ( [-OUT:ort|ott|oett]), endgaps are filled up with this character.

Default is (a blank). When producing an output in HTML format ( [-OUT:orh|oth|oeth]), end-gaps are filled up with this character.

File of filenames containing the names of the experiment or phd files to assemble when the [-LR:ft=FOFNEXP] option is used. One filename per line, blank lines accepted, lines starting with a hash (#) are treated as comment lines, nothing else. Use [-FN:fofnin] to change the default name.

File containing the sequences (and their qualities) to assemble in PHD format.

File containing sequences and ...

... file containing quality values of sequences for the assembly in FASTA format.

FASTQ file containing sequences and qualities. MIRA automatically recognises Sanger FASTQ format (base quality offset = 33) and newer Illumina FASTQ format (base quality offset = 64). Old Illumina FASTQ format with negative base qualities (base offset < 64) is not supported anymore).

File containing the sequences (and their qualities) to assemble in CAF format. This format also may contain the result of an assembly (the contig consensus sequences).

Assembled project written in type = (gap4da / caf / ace / fasta / html / tcs / wig / text) format by mira, final result.

Type gap4da is a directory containing experiment files and a file of filenames (called 'fofn'), all other types are files. gap4da, caf, ace contain the complete assembly information suitable for import into different post-processing tools (gap4, consed and others). html and text contain visual representations of the assembly suited for viewing in browsers or as simple text file. tcs is a summary of a contig suited for "quick" analyses from command-line tools or even visual inspection. wig is a file containing coverage information (useful for mapping assemblies) which can be loaded and shown by different genome browsers (IGB, GMOD, USCS and probably many more.

fasta contains the contig consensus sequences (and .fasta.qual the consensus qualities). Please note that they come in two flavours: padded and unpadded. The padded versions may contains stars (*) denoting gap base positions where there was some minor evidence for additional bases, but not strong enough to be considered as a real base. Unpadded versions have these gaps removed. Padded versions have an additional postfix .padded, while unpadded versions do not have a special postfix.

This file contains basic information about the assembly. MIRA will split the information in two parts: information about large contigs and information about all contigs.

For more information on how to interpret this file, please consult the chapter on "Results" of the MIRA documentation manual.

	Note
	In contrast to other information files, this file appears always in the "info" directory, even when just intermediate results are reported.

This file contains information which reads have been assembled into which contigs (or singlets).

This file contains statistics about the contigs themselves, their length, average consensus quality, number of reads, maximum and average coverage, average read length, number of A, C, G, T, N, X and gaps in consensus.

This file contains information about the tags (and their position) that are present in the consensus of a contig.

Tab delimited file with three columns: read name, repeat level tag, sequence.

This file permits a quick analysis of the repetitiveness of different parts of reads in a project. See [-SK:rliif] to control from which repetitive level on subsequences of reads are written to this file,

	Note
	Reads can have more than one entry in this file. E.g., with standard settings (-SK:rliif=6) if the start of a read is covered by MNRr, followed by a HAF3 region and finally the read ends with HAF6, then there will be two lines in the file: one for the subsequence covered by MNRr, one for HAF6.

A list containing the names of those reads that have been sorted out of the assembly before any processing started only due to the fact that they were too short.

This file contains information about the tags and their position that are present in each read. The read positions are given relative to the forward direction of the sequence (i.e. as it was entered into the the assembly).

A list of sequences that have been found to be invalid due to various reasons (given in the output of the assembler).