OS | Sync Package List | Search | Install |
---|---|---|---|
Ubuntu, Mint, Debian | apt-get update | apt-cache search tbb | apt-get install libtbb-dev |
Fedora, CentOS | yum check-update | yum search tbb | yum install tbb-devel.x86_64 |
Arch | packman -Sy | pacman -Ss tbb | pacman -S extra/intel-tbb |
Gentoo | emerge --sync | emerge --search tbb | emerge dev-cpp/tbb |
MacOS | brew update | brew search tbb | brew install tbb |
FreeBSD | portsnap fetch update | make search name=tbb | cd /usr/ports/devel/tbb && make install && make clean |
-x | The basename of the index for the reference genome. The basename is the name of any of the index files up to but not including the final `.1.bt2` / `.rev.1.bt2` / etc. `bowtie2` looks for the specified index first in the current directory, then in the directory specified in the `BOWTIE2_INDEXES` environment variable. |
-1 |
Comma-separated list of files containing mate 1s (filename usually includes
`_1`), e.g. `-1 flyA_1.fq,flyB_1.fq`. Sequences specified with this option must
correspond file-for-file and read-for-read with those specified in ` |
-2 |
Comma-separated list of files containing mate 2s (filename usually includes
`_2`), e.g. `-2 flyA_2.fq,flyB_2.fq`. Sequences specified with this option must
correspond file-for-file and read-for-read with those specified in ` |
-U | Comma-separated list of files containing unpaired reads to be aligned, e.g. `lane1.fq,lane2.fq,lane3.fq,lane4.fq`. Reads may be a mix of different lengths. If `-` is specified, `bowtie2` gets the reads from the "standard in" or "stdin" filehandle. |
-S | File to write SAM alignments to. By default, alignments are written to the "standard out" or "stdout" filehandle (i.e. the console). |
-q |
Reads (specified with ` |
--interleaved | Reads interleaved FASTQ files where the first two records (8 lines) represent a mate pair. |
--tab5 | Each read or pair is on a single line. An unpaired read line is `[name]\t[seq]\t[qual]\n`. A paired-end read line is `[name]\t[seq1]\t[qual1]\t[seq2]\t[qual2]\n`. An input file can be a mix of unpaired and paired-end reads and Bowtie 2 recognizes each according to the number of fields, handling each as it should. |
--tab6 | Similar to [`--tab5`] except, for paired-end reads, the second end can have a different name from the first: `[name1]\t[seq1]\t[qual1]\t[name2]\t[seq2]\t[qual2]\n` |
--qseq |
Reads (specified with ` |
-f |
Reads (specified with ` |
-r |
Reads (specified with ` |
-F k: |
Reads are substrings (k-mers) extracted from a FASTA file ` |
-c |
The read sequences are given on command line. I.e. ` |
-s/--skip |
Skip (i.e. do not align) the first ` |
-u/--qupto |
Align the first ` |
-5/--trim5 |
Trim ` |
-3/--trim3 |
Trim ` |
--trim-to [3:|5:] |
Trim reads exceeding ` |
--phred33 | Input qualities are ASCII chars equal to the [Phred quality] plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines. |
--phred64 | Input qualities are ASCII chars equal to the [Phred quality] plus 64. This is also called the "Phred+64" encoding. |
--solexa-quals | Convert input qualities from [Solexa][Phred quality] (which can be negative) to [Phred][Phred quality] (which can't). This scheme was used in older Illumina GA Pipeline versions (prior to 1.3). Default: off. |
--int-quals | Quality values are represented in the read input file as space-separated ASCII integers, e.g., `40 40 30 40`..., rather than ASCII characters, e.g., `II?I`.... Integers are treated as being on the [Phred quality] scale unless [`--solexa-quals`] is also specified. Default: off. |
--very-fast | Same as: `-D 5 -R 1 -N 0 -L 22 -i S,0,2.50` |
--fast | Same as: `-D 10 -R 2 -N 0 -L 22 -i S,0,2.50` |
--sensitive | Same as: `-D 15 -R 2 -L 22 -i S,1,1.15` (default in [`--end-to-end`] mode) |
--very-sensitive | Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50` |
--very-fast-local | Same as: `-D 5 -R 1 -N 0 -L 25 -i S,1,2.00` |
--fast-local | Same as: `-D 10 -R 2 -N 0 -L 22 -i S,1,1.75` |
--sensitive-local | Same as: `-D 15 -R 2 -N 0 -L 20 -i S,1,0.75` (default in [`--local`] mode) |
--very-sensitive-local | Same as: `-D 20 -R 3 -N 0 -L 20 -i S,1,0.50` |
-N | Sets the number of mismatches to allowed in a seed alignment during [multiseed alignment]. Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower) but increases sensitivity. Default: 0. |
-L | Sets the length of the seed substrings to align during [multiseed alignment]. Smaller values make alignment slower but more sensitive. Default: the [`--sensitive`] preset is used by default, which sets `-L` to 20 both in [`--end-to-end`] mode and in [`--local`] mode. |
-i | Sets a function governing the interval between seed substrings to use during [multiseed alignment]. For instance, if the read has 30 characters, and seed length is 10, and the seed interval is 6, the seeds extracted will be: Read: TAGCTACGCTCTACGCTATCATGCATAAAC Seed 1 fw: TAGCTACGCT Seed 1 rc: AGCGTAGCTA Seed 2 fw: CGCTCTACGC Seed 2 rc: GCGTAGAGCG Seed 3 fw: ACGCTATCAT Seed 3 rc: ATGATAGCGT Seed 4 fw: TCATGCATAA Seed 4 rc: TTATGCATGA Since it's best to use longer intervals for longer reads, this parameter sets the interval as a function of the read length, rather than a single one-size-fits-all number. For instance, specifying `-i S,1,2.5` sets the interval function `f` to `f(x) = 1 + 2.5 * sqrt(x)`, where x is the read length. See also: [setting function options]. If the function returns a result less than 1, it is rounded up to 1. Default: the [`--sensitive`] preset is used by default, which sets `-i` to `S,1,1.15` in [`--end-to-end`] mode to `-i S,1,0.75` in [`--local`] mode. |
--n-ceil | Sets a function governing the maximum number of ambiguous characters (usually `N`s and/or `.`s) allowed in a read as a function of read length. For instance, specifying `-L,0,0.15` sets the N-ceiling function `f` to `f(x) = 0 + 0.15 * x`, where x is the read length. See also: [setting function options]. Reads exceeding this ceiling are [filtered out]. Default: `L,0,0.15`. |
--dpad |
"Pads" dynamic programming problems by ` |
--gbar |
Disallow gaps within ` |
--ignore-quals | When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value. I.e. input is treated as though all quality values are high. This is also the default behavior when the input doesn't specify quality values (e.g. in [`-f`], [`-r`], or [`-c`] modes). |
--nofw/--norc | If `--nofw` is specified, `bowtie2` will not attempt to align unpaired reads to the forward (Watson) reference strand. If `--norc` is specified, `bowtie2` will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, `--nofw` and `--norc` pertain to the fragments; i.e. specifying `--nofw` causes `bowtie2` to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default: both strands enabled. |
--no-1mm-upfront | By default, Bowtie 2 will attempt to find either an exact or a 1-mismatch end-to-end alignment for the read *before* trying the [multiseed heuristic]. Such alignments can be found very quickly, and many short read alignments have exact or near-exact end-to-end alignments. However, this can lead to unexpected alignments when the user also sets options governing the [multiseed heuristic], like [`-L`] and [`-N`]. For instance, if the user specifies `-N 0` and `-L` equal to the length of the read, the user will be surprised to find 1-mismatch alignments reported. This option prevents Bowtie 2 from searching for 1-mismatch end-to-end alignments before using the [multiseed heuristic], which leads to the expected behavior when combined with options such as [`-L`] and [`-N`]. This comes at the expense of speed. |
--end-to-end | In this mode, Bowtie 2 requires that the entire read align from one end to the other, without any trimming (or "soft clipping") of characters from either end. The match bonus [`--ma`] always equals 0 in this mode, so all alignment scores are less than or equal to 0, and the greatest possible alignment score is 0. This is mutually exclusive with [`--local`]. `--end-to-end` is the default mode. |
--local | In this mode, Bowtie 2 does not require that the entire read align from one end to the other. Rather, some characters may be omitted ("soft clipped") from the ends in order to achieve the greatest possible alignment score. The match bonus [`--ma`] is used in this mode, and the best possible alignment score is equal to the match bonus ([`--ma`]) times the length of the read. Specifying `--local` and one of the presets (e.g. `--local --very-fast`) is equivalent to specifying the local version of the preset (`--very-fast-local`). This is mutually exclusive with [`--end-to-end`]. `--end-to-end` is the default mode. |
--ma |
Sets the match bonus. In [`--local`] mode ` |
--mp MX,MN | Sets the maximum (`MX`) and minimum (`MN`) mismatch penalties, both integers. A number less than or equal to `MX` and greater than or equal to `MN` is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an `N`. If [`--ignore-quals`] is specified, the number subtracted quals `MX`. Otherwise, the number subtracted is `MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) )` where Q is the Phred quality value. Default: `MX` = 6, `MN` = 2. |
--np | Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as `N`. Default: 1. |
--rdg |
Sets the read gap open (` |
--rfg |
Sets the reference gap open (` |
--score-min | Sets a function governing the minimum alignment score needed for an alignment to be considered "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying `L,0,-0.6` sets the minimum-score function `f` to `f(x) = 0 + -0.6 * x`, where `x` is the read length. See also: [setting function options]. The default in [`--end-to-end`] mode is `L,-0.6,-0.6` and the default in [`--local`] mode is `G,20,8`. |
-k |
By default, `bowtie2` searches for distinct, valid alignments for each read.
When it finds a valid alignment, it continues looking for alignments that are
nearly as good or better. The best alignment found is reported (randomly
selected from among best if tied). Information about the best alignments is
used to estimate mapping quality and to set SAM optional fields, such as
[`AS:i`] and [`XS:i`].
When `-k` is specified, however, `bowtie2` behaves differently. Instead, it
searches for at most ` |
-a | Like [`-k`] but with no upper limit on number of alignments to search for. `-a` is mutually exclusive with [`-k`]. Note: Bowtie 2 is not designed with `-a` mode in mind, and when aligning reads to long, repetitive genomes this mode can be very, very slow. |
-D |
Up to ` |
-R |
` |
-I/--minins | The minimum fragment length for valid paired-end alignments. E.g. if `-I 60` is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as [`-X`][`+X`] is also satisfied). A 19-bp gap would not be valid in that case. If trimming options [`-3`] or [`-5`] are also used, the [`-I`][`+I`] constraint is applied with respect to the untrimmed mates. The larger the difference between [`-I`][`+I`] and [`-X`][`+X`], the slower Bowtie 2 will run. This is because larger differences between [`-I`][`+I`] and [`-X`][`+X`] require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. Default: 0 (essentially imposing no minimum) |
-X/--maxins | The maximum fragment length for valid paired-end alignments. E.g. if `-X 100` is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as [`-I`][`+I`] is also satisfied). A 61-bp gap would not be valid in that case. If trimming options [`-3`] or [`-5`] are also used, the `-X` constraint is applied with respect to the untrimmed mates, not the trimmed mates. The larger the difference between [`-I`][`+I`] and [`-X`][`+X`], the slower Bowtie 2 will run. This is because larger differences between [`-I`][`+I`] and [`-X`][`+X`] require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient. Default: 500. |
--fr/--rf/--ff | The upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand. E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints ([`-I`][`+I`] and [`-X`][`+X`]) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. ` --ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented. Default: `--fr` (appropriate for Illumina's Paired-end Sequencing Assay). |
--no-mixed | By default, when `bowtie2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. This option disables that behavior. |
--no-discordant | By default, `bowtie2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints ([`--fr`/`--rf`/`--ff`], [`-I`][`+I`], [`-X`][`+X`]). This option disables that behavior. |
--dovetail | If the mates "dovetail", that is if one mate alignment extends past the beginning of the other such that the wrong mate begins upstream, consider that to be concordant. See also: [Mates can overlap, contain or dovetail each other]. Default: mates cannot dovetail in a concordant alignment. |
--no-contain | If one mate alignment contains the other, consider that to be non-concordant. See also: [Mates can overlap, contain or dovetail each other]. Default: a mate can contain the other in a concordant alignment. |
--no-overlap | If one mate alignment overlaps the other at all, consider that to be non-concordant. See also: [Mates can overlap, contain or dovetail each other]. Default: mates can overlap in a concordant alignment. |
-t/--time | Print the wall-clock time required to load the index files and align the reads. This is printed to the "standard error" ("stderr") filehandle. Default: off. |
--un |
Write unpaired reads that fail to align to file at ` |
--al |
Write unpaired reads that align at least once to file at ` |
--un-conc |
Write paired-end reads that fail to align concordantly to file(s) at ` |
--al-conc |
Write paired-end reads that align concordantly at least once to file(s) at
` |
--quiet | Print nothing besides alignments and serious errors. |
--met-file |
Write `bowtie2` metrics to file ` |
--met-stderr | Write `bowtie2` metrics to the "standard error" ("stderr") filehandle. This is not mutually exclusive with [`--met-file`]. Having alignment metric can be useful for debugging certain problems, especially performance issues. See also: [`--met`]. Default: metrics disabled. |
--met |
Write a new `bowtie2` metrics record every ` |
--no-unal | Suppress SAM records for reads that failed to align. |
--no-hd | Suppress SAM header lines (starting with `@`). |
--no-sq | Suppress `@SQ` SAM header lines. |
--rg-id |
Set the read group ID to ` |
--rg |
Add ` |
--omit-sec-seq | When printing secondary alignments, Bowtie 2 by default will write out the `SEQ` and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterisk in those fields instead. |
--soft-clipped-unmapped-tlen | Consider soft-clipped bases unmapped when calculating `TLEN`. Only available in [`--local`] mode. |
--sam-no-qname-trunc | Suppress standard behavior of truncating readname at first whitespace at the expense of generating non-standard SAM |
--xeq | Use `'='/'X'`, instead of `'M'`, to specify matches/mismatches in SAM record |
-o/--offrate |
Override the offrate of the index with ` |
-p/--threads NTHREADS | Launch `NTHREADS` parallel search threads (default: 1). Threads will run on separate processors/cores and synchronize when parsing reads and outputting alignments. Searching for alignments is highly parallel, and speedup is close to linear. Increasing `-p` increases Bowtie 2's memory footprint. E.g. when aligning to a human genome index, increasing `-p` from 1 to 8 increases the memory footprint by a few hundred megabytes. This option is only available if `bowtie` is linked with the `pthreads` library (i.e. if `BOWTIE_PTHREADS=0` is not specified at build time). |
--reorder | Guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when [`-p`] is set greater than 1. Specifying `--reorder` and setting [`-p`] greater than 1 causes Bowtie 2 to run somewhat slower and use somewhat more memory than if `--reorder` were not specified. Has no effect if [`-p`] is set to 1, since output order will naturally correspond to input order in that case. |
--mm | Use memory-mapped I/O to load the index, rather than typical file I/O. Memory-mapping allows many concurrent `bowtie` processes on the same computer to share the same memory image of the index (i.e. you pay the memory overhead just once). This facilitates memory-efficient parallelization of `bowtie` in situations where using [`-p`] is not possible or not preferable. |
--qc-filter | Filter out reads for which the QSEQ filter field is non-zero. Only has an effect when read format is [`--qseq`]. Default: off. |
--seed |
Use ` |
--non-deterministic | Normally, Bowtie 2 re-initializes its pseudo-random generator for each read. It seeds the generator with a number derived from (a) the read name, (b) the nucleotide sequence, (c) the quality sequence, (d) the value of the [`--seed`] option. This means that if two reads are identical (same name, same nucleotides, same qualities) Bowtie 2 will find and report the same alignment(s) for both, even if there was ambiguity. When `--non-deterministic` is specified, Bowtie 2 re-initializes its pseudo-random generator for each read using the current time. This means that Bowtie 2 will not necessarily report the same alignment for two identical reads. This is counter-intuitive for some users, but might be more appropriate in situations where the input consists of many identical reads. |
--version | Print version information and quit. |
-h/--help | Print usage information and quit. |
1 | The read is one of a pair |
2 | The alignment is one end of a proper paired-end alignment |
4 | The read has no reported alignments |
8 | The read is one of a pair and has no reported alignments |
16 | The alignment is to the reverse reference strand |
32 | The other mate in the paired-end alignment is aligned to the reverse reference strand |
64 | The read is mate 1 in a pair |
128 | The read is mate 2 in a pair |
AS:i: | Alignment score. Can be negative. Can be greater than 0 in [`--local`] mode (but not in [`--end-to-end`] mode). Only present if SAM record is for an aligned read. |
XS:i: | Alignment score for the best-scoring alignment found other than the alignment reported. Can be negative. Can be greater than 0 in [`--local`] mode (but not in [`--end-to-end`] mode). Only present if the SAM record is for an aligned read and more than one alignment was found for the read. Note that, when the read is part of a concordantly-aligned pair, this score could be greater than [`AS:i`]. |
YS:i: | Alignment score for opposite mate in the paired-end alignment. Only present if the SAM record is for a read that aligned as part of a paired-end alignment. |
XN:i: | The number of ambiguous bases in the reference covering this alignment. Only present if SAM record is for an aligned read. |
XM:i: | The number of mismatches in the alignment. Only present if SAM record is for an aligned read. |
XO:i: | The number of gap opens, for both read and reference gaps, in the alignment. Only present if SAM record is for an aligned read. |
XG:i: | The number of gap extensions, for both read and reference gaps, in the alignment. Only present if SAM record is for an aligned read. |
NM:i: | The edit distance; that is, the minimal number of one-nucleotide edits (substitutions, insertions and deletions) needed to transform the read string into the reference string. Only present if SAM record is for an aligned read. |
YF:Z: | String indicating reason why the read was filtered out. See also: [Filtering]. Only appears for reads that were filtered out. |
YT:Z: | Value of `UU` indicates the read was not part of a pair. Value of `CP` indicates the read was part of a pair and the pair aligned concordantly. Value of `DP` indicates the read was part of a pair and the pair aligned discordantly. Value of `UP` indicates the read was part of a pair but the pair failed to aligned either concordantly or discordantly. |
MD:Z: | A string representation of the mismatched reference bases in the alignment. See [SAM Tags format specification][SAMTags] for details. Only present if SAM record is for an aligned read. |
|
A comma-separated list of [`FASTA`] files containing the reference sequences to be
aligned to, or, if [`-c`](#bowtie2-build-options-c) is specified, the sequences
themselves. E.g., ` |
|
The basename of the index files to write. By default, `bowtie2-build` writes
files named `NAME.1.bt2`, `NAME.2.bt2`, `NAME.3.bt2`, `NAME.4.bt2`,
`NAME.rev.1.bt2`, and `NAME.rev.2.bt2`, where `NAME` is ` |
-f |
The reference input files (specified as ` |
-c |
The reference sequences are given on the command line. I.e. ` |
--large-index | Force `bowtie2-build` to build a [large index](#small-and-large-indexes), even if the reference is less than ~ 4 billion nucleotides inlong. |
-a/--noauto | Disable the default behavior whereby `bowtie2-build` automatically selects values for the [`--bmax`], [`--dcv`] and [`--packed`] parameters according to available memory. Instead, user may specify values for those parameters. If memory is exhausted during indexing, an error message will be printed; it is up to the user to try new parameters. |
-p/--packed | Use a packed (2-bits-per-nucleotide) representation for DNA strings. This saves memory but makes indexing 2-3 times slower. Default: off. This is configured automatically by default; use [`-a`/`--noauto`] to configure manually. |
--bmax | The maximum number of suffixes allowed in a block. Allowing more suffixes per block makes indexing faster, but increases peak memory usage. Setting this option overrides any previous setting for [`--bmax`], or [`--bmaxdivn`]. Default (in terms of the [`--bmaxdivn`] parameter) is [`--bmaxdivn`] 4 * number of threads. This is configured automatically by default; use [`-a`/`--noauto`] to configure manually. |
--bmaxdivn | The maximum number of suffixes allowed in a block, expressed as a fraction of the length of the reference. Setting this option overrides any previous setting for [`--bmax`], or [`--bmaxdivn`]. Default: [`--bmaxdivn`] 4 * number of threads. This is configured automatically by default; use [`-a`/`--noauto`] to configure manually. |
--dcv |
Use ` |
--nodc | Disable use of the difference-cover sample. Suffix sorting becomes quadratic-time in the worst case (where the worst case is an extremely repetitive reference). Default: off. |
-r/--noref | Do not build the `NAME.3.bt2` and `NAME.4.bt2` portions of the index, which contain a bitpacked version of the reference sequences and are used for paired-end alignment. |
-3/--justref | Build only the `NAME.3.bt2` and `NAME.4.bt2` portions of the index, which contain a bitpacked version of the reference sequences and are used for paired-end alignment. |
-o/--offrate |
To map alignments back to positions on the reference sequences, it's necessary
to annotate ("mark") some or all of the [Burrows-Wheeler] rows with their
corresponding location on the genome.
[`-o`/`--offrate`](#bowtie2-build-options-o) governs how many rows get marked:
the indexer will mark every 2^` |
-t/--ftabchars |
The ftab is the lookup table used to calculate an initial [Burrows-Wheeler]
range with respect to the first ` |
--seed |
Use ` |
--cutoff |
Index only the first ` |
-q/--quiet | `bowtie2-build` is verbose by default. With this option `bowtie2-build` will print only error messages. |
--threads | By default `bowtie2-build` is using only one thread. Increasing the number of threads will speed up the index building considerably in most cases. |
-h/--help | Print usage information and quit. |
--version | Print version information and quit. |
| The basename of the index to be inspected. The basename is name of any of the index files but with the `.X.bt2` or `.rev.X.bt2` suffix omitted. `bowtie2-inspect` first looks in the current directory for the index files, then in the directory specified in the `BOWTIE2_INDEXES` environment variable. |
-a/--across |
When printing [`FASTA`] output, output a newline character every ` |
-n/--names | Print reference sequence names, one per line, and quit. |
-s/--summary |
Print a summary that includes information about index settings, as well as the
names and lengths of the input sequences. The summary has this format:
Colorspace <0 or 1>
SA-Sample 1 in |
-v/--verbose | Print verbose output (for debugging). |
--version | Print version information and quit. |
-h/--help | Print usage information and quit. |