QUAST 4.6.3 manual

--threads (or -t) <int>

Maximum number of threads. The default value is 25% of all available CPUs but not less than 1. If QUAST fails to determine the number of CPUs, maximum threads number is set to 4.

--labels (or -l) <label,label...>

Human-readable assembly names. Those names will be used in reports, plots and logs. For example:

-l SPAdes,IDBA-UD

If your labels include spaces, use quotes:

-l SPAdes,"Assembly 2",Assembly3

-l "SPAdes 2.5, SPAdes 2.4, IDBA-UD"

-L

Take assembly names from their parent directory names.

--gene-finding (or -f)

Enables gene finding. Affects performance, thus disabled by default.

By default, we assume that the genome is prokaryotic, and apply GeneMarkS for gene finding. If the genome is eukaryotic, use --eukaryote option to enable GeneMark-ES instead. If it is a metagenome (you are running metaquast.py), MetaGeneMark is used. You can also force MetaGeneMark predictions with --mgm option described below.

If a gene file is provided with -G as well, both # genes in the file covered by the assembly, and # predicted genes are reported. Note that operons are not predicted, but a file of known operon positions can be provided with -O.

--mgm

Force use of MetaGeneMark for gene finding (instead of the default finders: GeneMarkS or GeneMark-ES).
Note: if you are working with metagenome assemblies, we recommend to use metaquast.py instead of quast.py (it is in the same directory as quast.py).

--glimmer

Use GlimmerHMM for gene finding (instead of GeneMark family of tools). Note: you may skip --gene-finding option if --glimmer is specified.

--gene-thresholds <int,int,...>

Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool. The default value is 0,300,1500,3000. Note: this list is used only if --gene-finding or --glimmer option is specified.

--eukaryote (or -e)

Genome is eukaryotic. Affects gene finding and contig alignment:

For prokaryotes (which is default), GeneMarkS is used. For eukaryotes, GeneMark-ES is used.
By default, QUAST assumes that a genome is circular and correctly processes its linear representation. This options indicates that the genome is not circular.

--est-ref-size <int>

Estimated reference genome size (in bp) for computing NGx statistics. This value will be used only if a reference genome file is not specified (see -R option).

--gage

Starts QUAST in "GAGE mode" (see section 2.3). Note: in this case, you have to specify a reference genome with -R.

--contig-thresholds <int,int,...>

Comma-separated list of contig length thresholds (in bp). Used in # contigs ≥ x and total length (≥ x) metrics (see section 3). The default value is 0,1000.

--scaffolds (or -s)

The assemblies are scaffolds (rather than contigs). QUAST will add split versions of assemblies to the comparison (named <assembly_name>_broken). Assemblies are split by continuous fragments of N's of length ≥ 10. If broken version is equal to the original assembly (i.e. nothing was split) it is not included in the comparison. Scaffold gap size misassemblies are enabled in this case (see section 3.1.2 for details and --scaffold-gap-max-size for setting maximum gap length).

--use-all-alignments (or -u)

Compute genome fraction, # genes, # operons metrics in the manner used in QUAST v.1.*. By default, QUAST v.2.0 and higher filters out ambiguous and redundant alignments, keeping only one alignment per contig (or one set of non-overlapping or slightly overlapping alignments). This option makes QUAST count all alignments.

--min-alignment (or -i) <int>

Minimum length of alignment (in bp). Alignments shorter than this value will be filtered. Note that all alignments shorter than 65 bp will be filtered regardless of this threshold.

--min-identity <float>

Minimum IDY% considered as proper alignment. Alignments with IDY% worse than this value will be filtered. Default is 95.0 %. Note that all alignments with IDY% less than 80.0% will be filtered regardless of this threshold.

--ambiguity-usage (or -a) <none|one|all>

Way of processing equally good alignments of a contig (probably repeats):

`none`	skip all such alignments;
`one`	take only one (the very best one);
`all`	use all alignments. Can cause a significant increase of # mismatches (repeats are almost always inexact due to accumulated SNPs, indels, etc.).

The default value is one.

The value all is useful for metagenomic assemblies where ambiguous alignments might represent homologous sequences of different strains. For that reason, --ambiguity-usage is set to all for the "combined reference" evaluation (see section 2.5). You may still modify this behaviour with --unique-mapping.

--ambiguity-score <float>

Score S for defining equally good alignments of a single contig (see --ambiguity-usage). All alignments are sorted by decreasing LEN × IDY% value. All alignments with LEN × IDY% less than S × best(LEN × IDY%) are discarded. S should be between 0.8 and 1.0. The default value is 0.99.

--strict-NA

Break contigs at every misassembly event (including local ones) to compute NAx and NGAx statistics. By default, QUAST breaks contigs only at extensive misassemblies (not local ones).

--extensive-mis-size (or -x) <int>

Lower threshold for the relocation size (gap or overlap size between left and right flanking sequence, see section 3.1.2 for details). Shorter relocations are considered as local misassemblies. It does not affect other types of extensive misassemblies (inversions and translocations). The default value is 1000 bp. Note that the threshold should be greater than maximum indel length which is 85 bp.

--scaffold-gap-max-size <int>

Max allowed scaffold gap length difference for detecting corresponding type of misassemblies (see section 3.1.2 for details). Longer inconsistencies are considered as relocations and thus, counted as extensive misassemblies. The default value is 10000 bp. Note that the threshold make sense only if it is greater than extensive misassembly size (see --extensive-mis-size, its default value is 1000 bp). Also note that scaffold gap size misassemblies are counted for scaffold assemblies only (use --scaffolds if your assemblies are scaffolds rather than contigs).

--unaligned-part-size <int>

Lower threshold for detecting partially unaligned contigs, see section 3.1.3 for details. The default value is 500 bp.

--fragmented

Reference genome is fragmented (e.g. a scaffold reference). QUAST will try to detect misassemblies caused by the fragmentation and mark them fake (will be excluded from # misassemblies). Note: QUAST will not detect misassemblies caused by the linear representation of circular genome.

--fragmented-max-indent <int>

Mark translocation as fake if both alignments are located no further than N bases from the ends of the reference fragments. The value should be less than extensive misassembly size (see --extensive-mis-size, its default value is 1000 bp). Default value is 85. Note: requires --fragmented option.

--plots-format <format>

File format for plots. Supported formats: emf, eps, pdf, png, ps, raw, rgba, svg, svgz. The default format is PDF.

--memory-efficient

Use one thread, separately per each assembly and each chromosome. This may significantly reduce memory consumption for large genomes. Note: this option will significantly slow down the processing as well.

--space-efficient

Create only primary output items (reports, plots, quast.log, etc). All auxiliary files (.stdout, .stderr, etc) will not be created. This may significantly reduce disk space usage on large assemblies (more than 100k contigs). Note: Icarus viewers also will not be built because they became enormously large and slow in case of zillions of contigs, thus not applicable.

--silent

Do not print detailed information about each step in standard output. This option does not affect quast.log file.

If an output path is not specified manually (with -o), QUAST generates its output into quast_results/result_<DATE> directory and creates latest symlink to it under quast_results/ directory.

QUAST output contains:

report.txt	assessment summary in plain text format,
report.tsv	tab-separated version of the summary, suitable for spreadsheets (Google Docs, Excel, etc),
report.tex	LaTeX version of the summary,
icarus.html	Icarus main menu with links to interactive viewers. See section 3.4 for details,
report.pdf	all other plots combined with all tables (file is created if matplotlib python library is installed),
report.html	HTML version of the report with interactive plots inside,
contigs_reports/
misassemblies_report	detailed report on misassemblies. See section 3.1.2 for details,
unaligned_report	detailed report on unaligned and partially unaligned contigs. See section 3.1.3 for details.

Note:

3.1 Metrics description

3.1.1 Summary report

# contigs (≥ x bp) is total number of contigs of length ≥ x bp. Not affected by the --min-contig parameter (see section 2.4).

Total length (≥ x bp) is the total number of bases in contigs of length ≥ x bp. Not affected by the --min-contig parameter (see section 2.4).

All remaining metrics are computed for contigs that exceed the threshold specified with --min-contig (see section 2.4, default is 500 bp).

# contigs is the total number of contigs in the assembly.

Largest contig is the length of the longest contig in the assembly.

Total length is the total number of bases in the assembly.

Reference length is the total number of bases in the reference genome.

GC (%) is the total number of G and C nucleotides in the assembly, divided by the total length of the assembly.

Reference GC (%) is the percentage of G and C nucleotides in the reference genome.

N50 is the length for which the collection of all contigs of that length or longer covers at least half an assembly.

NG50 is the length for which the collection of all contigs of that length or longer covers at least half the reference genome.
This metric is computed only if the reference genome is provided.

N75 and NG75 are defined similarly to N50 but with 75 % instead of 50 %.

L50 (L75, LG50, LG75) is the number of contigs equal to or longer than N50 (N75, NG50, NG75)
In other words, L50, for example, is the minimal number of contigs that cover half the assembly.

# misassemblies is the number of positions in the contigs (breakpoints) that satisfy one of the following criteria:

the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference;
flanking sequences overlap on more than 1 kbp;
flanking sequences align to different strands or different chromosomes;
flanking sequences align on different reference genomes (MetaQUAST only).

This metric requires a reference genome. Note that default threshold of 1 kbp can be changed with --extensive-mis-size. See more details about misassemblies in section 3.1.2. Important note: this metric does not sum up

# local misassemblies, # scaffold gap size misassemblies,
# structural variants

, and # unaligned mis. contigs described below.

# misassembled contigs is the number of contigs that contain misassembly events (see # misassemblies above).

Misassembled contigs length is the total number of bases in misassembled contigs.

# local misassemblies is the number of positions in the contigs (breakpoints) that satisfy the following conditions:

The gap or overlap between left and right flanking sequences is less than 1 kbp, and larger than the maximum indel length (85 bp).
The left and right flanking sequences both are on the same strand of the same chromosome of the reference genome.

Note that default threshold of 1 kbp can be changed with --extensive-mis-size.

# scaffold gap size misassemblies is the number of positions in the scaffolds (breakpoints) where the flanking sequences are combined in scaffold on the wrong distance (--scaffolds only). Max allowed distance inconsistency is controlled by --scaffold-gap-max-size option (default is 10 kbp).

# structural variants is the number of misassemblies matched with structural variations of genome (if reads or BEDPE file with SV are provided, see --reads1/reads2 and --sv-bedpe).

# unaligned mis. contigs is the number of contigs that have the number of unaligned bases more than 50% of contig length and at least one misassembly event in their aligned fragment. Such contigs are probably not related to the reference genome, thus their misassemblies may be not real errors but differences between the assembled organism and the reference.

# unaligned contigs is the number of contigs that have no alignment to the reference sequence. The value "X + Y part" means X totally unaligned contigs plus Y partially unaligned contigs. This metric sums up # unaligned mis. contigs described above.

Unaligned length is the total length of all unaligned regions in the assembly (sum of lengths of fully unaligned contigs and unaligned parts of partially unaligned ones).

Genome fraction (%) is the percentage of aligned bases in the reference genome. A base in the reference genome is aligned if there is at least one contig with at least one alignment to this base. Contigs from repetitive regions may map to multiple places, and thus may be counted multiple times (see --ambiguity-usage).

Duplication ratio is the total number of aligned bases in the assembly divided by the total number of aligned bases in the reference genome (see Genome fraction (%) for the 'aligned base' definition). If the assembly contains many contigs that cover the same regions of the reference, its duplication ratio may be much larger than 1. This may occur due to overestimating repeat multiplicities and due to small overlaps between contigs, among other reasons.

# N's per 100 kbp is the average number of uncalled bases (N's) per 100000 assembly bases.

# mismatches per 100 kbp is the average number of mismatches per 100000 aligned bases. True SNPs and sequencing errors are not distinguished and are counted equally.

# indels per 100 kbp is the average number of indels per 100000 aligned bases. Several consecutive single nucleotide indels are counted as one indel.

# genes is the number of genes in the assembly (complete and partial), based on a user-provided list of gene positions in the reference genome. A gene 'partially covered' if the assembly contains at least 100 bp of this gene but not the whole one.

This metric is computed only if a reference genome and an annotated list of gene positions are provided (see section 2.4).

# operons is defined similarly to # genes, but an operon positions file required instead.

# predicted genes is the number of genes in the assembly found by GeneMarkS, GeneMark-ES, MetaGeneMark, or GlimmerHMM. See the description of --gene-finding option for details.

Total aligned length is the total number of aligned bases in the assembly. A value is usually smaller than a value of total length because some of the contigs may be unaligned or partially unaligned.

Largest alignment is the length of the largest continuous alignment in the assembly. A value can be smaller than a value of largest contig if the largest contig is misassembled or partially unaligned.

NA50, NGA50, NA75, NGA75, LA50, LA75, LGA50, LGA75 ("A" stands for "aligned") are similar to the corresponding metrics without "A", but in this case aligned blocks instead of contigs are considered.
Aligned blocks are obtained by breaking contigs at misassembly events and removing all unaligned bases.

3.1.2 Misassemblies report

# misassemblies is the same as # misassemblies from section 3.1.1. However, this report also contains a classification of all misassembly events into three groups: relocations, translocations, and inversions (see below). For metagenomic assemblies, this classification also includes interspecies translocation.

Relocation is a misassembly event (breakpoint) where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference genome, or they overlap by more than 1 kbp, and both flanking sequences align on the same chromosome. Note that default threshold of 1 kbp can be changed by --extensive-mis-size.

Translocation is a misassembly event (breakpoint) where the flanking sequences align on different chromosomes.

Interspecies translocation is a misassembly event (breakpoint) where the flanking sequences align on different reference genomes (MetaQUAST only).

Inversion is a misassembly event (breakpoint) where the flanking sequences align on opposite strands of the same chromosome.

# misassembled contigs and misassembled contigs length are the same as the metrics from section 3.1.1 and are counted among all contigs with any type of a misassembly event described above (relocation, translocation, interspecies translocation or inversion).

# possibly misassembled contigs is the number of contigs that contain large unaligned fragment and thus could possibly contain interspecies translocation with unknown reference (MetaQUAST only, combined reference only). Minimal length of the consecutive unaligned fragment (excluding N's) is controlled by --unaligned-part-size, default value is 500 bp.

# possible misassemblies is the number of putative interspecies translocations in possibly misassembled contigs if each large unaligned fragment is supposed to be a fragment of unknown reference (MetaQUAST only, combined reference only).

The next metrics are the same to homonymous metrics from section 3.1.1. Note that all of them are excluded from # misassemblies and related metrics:

# local misassemblies,
# scaffold gap size misassemblies,
# structural variants,
# unaligned mis. contigs.

# mismatches is the number of mismatches in all aligned bases.

# indels is the number of indels in all aligned bases. Several consecutive single nucleotide indels are counted as one indel. Note: default maximum length of indel is 85 bp. All indels larger than 85 bp are considered as local misassemblies.

# indels (≤ 5 bp) is the number of indels of length ≤ 5 bp.

# indels (> 5 bp) is the number of indels of length > 5 bp.

Indels length is the total number of bases contained in all indels.

3.1.3 Unaligned report

# fully unaligned contigs is the number of contigs that have no alignment to the reference sequence.

Fully unaligned length is the total number of bases in all unaligned contigs.

# partially unaligned contigs is the number of contigs that are not fully unaligned (i.e. have at least one alignment), but have at least one unaligned fragment ≥ the threshold defined by --unaligned-part-size (default value is 500 bp).

Partially unaligned length is the total number of unaligned bases in all partially unaligned contigs.

# N's is the total number of uncalled bases (N's) in the assembly.

3.2 Plots description

This section describes PDF and HTML plots. For Icarus interactive contig alignment and size visualization see section 3.4.

Cumulative length plot shows the growth of contig lengths. On the x-axis, contigs are ordered from the largest to smallest. The y-axis gives the size of the x largest contigs in the assembly.

Nx plot shows Nx values as x varies from 0 to 100 %.

NGx plot shows NGx values as x varies from 0 to 100 %.

GC content plot shows the distribution of GC content in the contigs.

The x value is the GC percentage (0 to 100 %).
The y value is the number of non-overlapping 100 bp windows which GC content equals x %.

For a single genome, the distribution is typically Gaussian. However, for assemblies with contaminants, the GC distribution appears to be a superposition of Gaussian distributions, giving a plot with multiple peaks.

GC content plot (by contigs) shows the distribution of # contigs with GC percentage in a certain range.

The x value is the GC percentage intervals (width is 5 %).
The y value is the number of contigs which GC content lies in the corresponding interval.

These plots are particularly useful for looking at metagenome assemblies, but also a potential good indicator of contamination for single organism assemblies.

Coverage histogram shows distribution of total contig lengths (y-axis) at different read coverage depths (x-axis, grouped in bins). Coverage bin size is automatically selected based on the number of contigs and coverage deviation.
Note: these histograms are only available for assemblies with SPAdes/Velvet-like contig naming style (..._length_X_cov_Y_...).

Cumulative length plot for aligned contigs shows the growth of lengths of aligned blocks. If a contig has a misassembly event, QUAST breaks it into smaller pieces called aligned blocks.

On the x-axis, blocks are ordered from the largest to smallest. The y-axis gives the size of the x largest aligned blocks.
This plot is created only if a reference genome is provided.

NAx and NGAx plots
These plots are similar to the Nx and NGx plots but for the NAx and NGAx metrics respectively. These plots are created only if a reference genome is provided.

Genes plot shows the growth rate of full genes in assemblies.
The y-axis is the number of full genes in the assembly, and the x-axis is the number of contigs in the assembly (from the largest one to the smallest one).
This plot could be created only if a reference genome and genes annotations files are given.

Operons plot is similar to the previous one but for operons.

Feature-Response Curves (FRCurves)
Our FRCurves are inspired by AMOS FRCurve definition: Given any such set of features, the response (quality) of the assembler output is then analyzed as a function of the maximum number of possible errors (features) allowed in the contigs. We plot FRCurves as following:
The x value (Feature space) is the total maximum number of features in the contigs.
The y value (Genome coverage %) is the total number of aligned bases in the contigs, divided by the reference length.

Note: since some contigs may overlap with other contigs or map to the same regions of the reference (see Duplication ratio), the total number of aligned bases may exceed the reference length and cause Genome coverage % larger than 100%.

FRCurves plots are currently available for # misassemblies (both PDF and interactive HTML formats) and # genes/operons (PDF version only). We probably will extend this set in the future.

MUMmer plots
MUMmer plots are alignment dotplots where a sequence is laid out on each axis and a point is plotted at every position where the two sequences show similarity. See mummerplot utility description for more details.
Note: these plots are saved to <quast_output_dir>/contigs_reports/<assembly_name>_mummerplot.html, as gnuplot requires additional dependencies for outputting in PDF/PNG and many other image formats. However, this type of plots is suppresed by --no-plots option (as other plots) and NOT suppressed by --no-html.

3.3 MetaQUAST output

Output for combined reference genome is located inside combined_reference subdirectory of the output directory provided with -o (or in quast_results/latest). An output for each reference genome is placed into separate directory inside <quast_output_dir>/runs_per_reference directory. Also, plots and reports for key metrics are saved under <quast_output_dir>/summary/. Combined HTML report is saved to <quast_output_dir>/report.html.

Metric-level plots
These plots are created for each key metric to show its values for all assemblies vs all reference genomes. References on the plot are sorted by the mean value of this metric in all assemblies. References are always sorted from the best results to the worst ones, thus the plot can be descending or ascending depend on the metric.

Metric-level reports (TXT, TSV and TEX versions)
These files contain the same information as the metric-level plots, but in different formats: simple text format, tab-separated format, and LaTeX.

Summary HTML-report
Summary HTML-report is created on the basis of HTML-report in combined_quast_output/. Each row is expandable and contains data for all reference genomes. You can view results separately for each reference genome by clicking on a row preceded by plus sign:

Note that values for some metrics like # contigs may not sum up, because one contig may be aligned to multiple reference genomes.

Krona charts
Krona pie charts show assemblies and dataset taxonomic profiles. Relative species abundance is calculated based on the total aligned length of contigs aligned to corresponding reference genome. Charts are created for each assembly and one additional chart is created for all assemblies altogether.
Note: these plots are created only in de novo evaluation mode (MetaQUAST without reference genomes).

3.4 Icarus output

Icarus generates contig size viewer and one or more contig alignment viewers (if reference genome/genomes are provided). All of them are located in <quast_output_dir>/icarus_viewers/. The links to the viewers and other auxiliary information are provided in Icarus main menu which is saved in <quast_output_dir>/icarus.html. Note that QUAST HTML report also contains a link to Icarus output.

All Icarus viewers contain a legend with color scheme description. For moving and zooming interactive window you can use mouse, Icarus controls (top panel) or keyboard shortcuts (+, -, ←, →, use Shift to speed up the action).

Contig size viewer
This type of viewer draws contigs ordered from longest to shortest. This ordering is suitable for comparing only largest contigs or number of contigs longer than a specific threshold. The viewer shows N50 and N75 with color and textual indication. If the reference genome is available or at least approximate genome length is known (see --est-ref-size), NG50 and NG75 are also shown. You can also tone down contigs shorter than a specified threshold using Icarus control panel.

Contig alignment viewer
This type of viewer is available only if a reference genome is provided. For large genomes (≥ 50 Mbp) each chromosome is displayed in a separate viewer. This is also true for multiple reference genomes (see section 2.5).
The viewer places contigs according to their mapping to the reference genome. The viewer can additionally visualize genes, operons, and read coverage distribution along the genome, if any of those were fed to QUAST.

Note: We recommend to use Icarus in Chrome, however it was tested in other popular web browsers as well (see FAQ, Q9 for the exact list with versions).

4. Adjusting QUAST reports and plots

You can easily change content, order of metrics, and metric names in all QUAST reports. In order to do this, edit CONFIGURABLE PARAMETERS section in quast_libs/reporting.py. It contains a lot of informative comments, which will help you to adjust QUAST reports easily even if you are new to Python.

You can also adjust plot colors, style and width of lines, legend font, etc. See CONFIGURABLE PARAMETERS section in quast_libs/plotter.py.

Note: if you restart QUAST on the same directory with new parameters, is will reuse existing alignments and run much faster. See the description of -o option in section 2.4.

5. Citation

6. Feedback and bug reports

We will be thankful if you help us make QUAST better by sending your comments, bug reports, and suggestions to quast.support@cab.spbu.ru.

We kindly ask you to attach the quast.log file from output directory (or an entire archive of the folder) if you have troubles running QUAST.

Note that if you didn't specify the output directory manually, it is going to be automatically set to quast_results/results_<date_time>, with a symbolic link quast_results/latest to that directory.

7. FAQ

This section contains frequent questions about QUAST. Read answers below for deeper understanding of the results generated by the tool.

For the simplicity of explanation we further refer to the directory containing all results as <quast_output_dir>.
If you use the command-line version of QUAST you can specify <quast_output_dir> with -o option ("quast_results/latest" if not specified).
If you use http://quast.bioinf.spbau.ru/ you should download full report by pressing "Download report" button (at the top-right corner), decompress result and go to "full_report" subdirectory.

FAQ Table of Contents

Q1. It seems that QUAST is giving me a differing number of misassemblies and misassembled contigs. Does this imply that QUAST looks for multiple misassemblies within one contig?

Yes, you are right, QUAST looks for multiple misassembly events within one contig. Thus, number of misassembled contigs is always less or equal to number of misassemblies.

Yes, there is such way.
QUAST copies all misassembled contigs of "<assembly_name>" assembly into <quast_output_dir>/contigs_reports/<assembly_name>.mis_contigs.fa file.
E.g. if your assembly is "contigs.fasta" then the file is "contigs.mis_contigs.fa", if your assembly is "ecoli_assembly_1.fa.gz" then the file is "ecoli_assembly_1.mis_contigs.fa".

Q3. Is it possible to find which misassembly corresponds to each contig and which kind of a misassembly event it is?

Yes, it is possible. QUAST produces report with detailed info about each contig alignments and the short version with only extensive misassemblies records.

Let's start with the short one. It is saved to <quast_output_dir>/contigs_reports/contigs_report_<assembly_name>.mis_contigs.info. E.g. if your assembly is "contigs.fasta" then the file is "contigs_report_contigs.mis_contigs.info", if your assembly is "ecoli_assembly_1.fasta" then the file is "contigs_report_ecoli_assembly_1.mis_contigs.info".
The content of this file looks like this:

Q4. Could you explain the format of Real Alignments in contigs report files (see the answer for Q3)?

There are two output files containing SNP information. Both of them are saved in <quast_output_dir>/contigs_reports/nucmer_output/ directory.
The first one has extension ".all_snps" and it is raw aligner output. Its format is:

Q6. What does "broken" version of an assembly refer to while assessing scaffolds' quality (--scaffolds option)?

Actually, the difference between "broken" and original assembly (scaffolds) is very simple. QUAST splits input fasta by continuous fragments of N's of length ≥ 10 and call this a "_broken" assembly. By doing this we try to reconstruct "contigs" which were used for construction of the scaffolds. After that, user can compare results for real scaffolds and "reconstructed contigs" and find out whether scaffolding step was useful or not.

If you have both contigs.fasta and scaffolds.fasta it is better to specify both files to QUAST and don't set --scaffolds option. The comparison of real contigs vs real scaffolds is more honest and informative than scaffolds vs scaffolds_broken.

To sum up, you should use --scaffolds option if you don't have original file with contigs but want to compare your scaffolds with it. Also note, that --scaffolds option implies QUAST to search for scaffold gap size misassemblies.

Q7. Can I add new assemblies to existing QUAST report without need to realign already processed assemblies? Or can I at least rerun existing QUAST report with slightly modified options set?

Yes, sure! You just need to specify existing QUAST output directory with -o option. Our tool will reuse already generated alignments and will run alignment process only for new assemblies. Note that all of QUAST options except --min-contig do not affect alignment process, so you can rerun previous QUAST command with modified options and QUAST will reuse existing alignments also.

Hint: if you did not specify QUAST output dir with -o option you can rerun QUAST on the same directory with -o quast_results/latest.

Q8. Which types of structural variations (SV) are handled by QUAST? Can you give examples of correct BEDPE files for --sv-bedpe option?

QUAST can detect and correctly resolve inversions, deletions, and translocations. We also plan to add support for insertions soon.

BEDPE format specification is here. We process first seven columns of the file (chrom1, start1, end1, chrom2, start2, end2, name), the rest are optional and not read by QUAST. Note that columns should be tab-separated!
Chrom1, start1, end1 define confidence interval around SV start, chrom2, start2, end2 define confidence interval around SV end. Name defines SV type and it should contain 'INV' substring for inversions or 'DEL' for deletions; translocations are automatically identified if chrom1 is not equal to chrom2.

Example of BEDPE line for inversion on positions 1000-1200 of 'E.coli' chromosome (confidence interval is 11 bp long):

We recommend to use Icarus in Chrome (tested with v49.0.x), however it also works properly in Safari (tested with v8.0.x) and Firefox (tested with v41.0.x and v45.0.x). Most of the functionality works in Internet Explorer 9 and higher, but we do not recommend this browser due to slow animation.

Q10. Could you show a sample file suitable for --references-list MetaQUAST option?

The file is just a list of reference names (one per line) to be searched in the NCBI database. Feel free to use spaces or underscores inside these names. Correct and working example is below:

Q11. Sometimes the "# contigs" and the "# contigs ≥ 0 bp" do not agree. Should not these be equal? What is the difference?

# contigs reports number of contigs above specified threshold. Default threshold is 500 bp and it can be changed with --min-contig option. Most of the other statistics are also based on all contigs larger than this threshold (we actually remove all shorts contigs in the beginning of the pipeline). For example, # misassemblies is essentially # misassemblies in contigs ≥ min-contig threshold.
However, all metrics containing length specification in parenthesis are not affected by --min-contig! For example, # contigs ≥ 0 bp is the number of contigs before the filtration.
The value of the threshold is written in the very first line of the text report (like "All statistics are based on contigs of size ≥ 500 bp, unless otherwise noted" ). It is also present in the header section of HTML report and on the bottom of PDF report.

To sum up, by default, # contigs is the same to # contigs >= 500 bp, so there will be difference between # contigs and # contigs ≥ 0 bp if your assembly has contigs shorter than 500 bp.

Q12. Can I use custom BLAST database instead of SILVA 16S rRNA for reference searching?

Yes. If you want to blast your contigs against a local BLAST database, you can specify path to the database with --blast-db option.
To create a BLAST database, you need makeblastdb from BLAST+ package. You can also use makeblastdb from <quast_installation_dir>/blast/ or ~/.quast/blast/ (depending on your installation). MetaQUAST automatically creates this directory and downloads the binary into it when you run full QUAST installation or metaquast.py without reference for the first time.
You can create a BLAST database from your FASTA file by running makeblastdb -in <path_to_fasta_file> -dbtype nucl. If you have multiple FASTA files, you should concatenate them into one.

Note: MetaQUAST will try to search references in the NCBI database based on headers from your FASTA file. Ensure that the headers contain species names in simple parsable format without spaces, for example:

Starting from v.4.4, we have added detailed reports with this information. These reports are generated for all assemblies and saved to <quast_output_dir>/contigs_reports/contigs_report_<assembly_name>.unaligned.info. E.g. if your assembly is "contigs.fasta" then the file is "contigs_report_contigs.unaligned.info", if your assembly is "ecoli_assembly_1.fasta" then the file is "contigs_report_ecoli_assembly_1.unaligned.info".

The report include all fully unaligned and partially unaligned contigs, i.e. contigs that have at least one unaligned fragment ≥ 500 bp. This is the default threshold and it can be changed with --unaligned-part-size option. The following values are reported for each contig:

Q14. I have very large assemblies and reference genome but my computational resources are limited. Could you recommend an optimal set of QUAST options to use?

Current QUAST version is not optimised for large genomes yet. However, we have some useful suggestions. You may be interested in adding the following options to your command line to reduce RAM consumption, disk space usage, and running time. Note that each of them have some negative effect, so you should choose what is more important for you and may be try them one by one until you find the optimal set for your particular case.

Q15. I evaluated my assembly using --scaffolds option but got counter-intuitive results. The number of misassemblies in "broken" version of the assembly is higher than in the original one while I expected vice versa or at max the similar numbers of misassemblies. Could you explain this?

You are absolutely right that normally a broken version of an assembly should have smaller (or the same) number of misassemblies comparing to the scaffolded version. Scaffolding is an additional step and it could introduce new errors by connecting not related contigs into a single scaffold. At the same time it could not fix misassemblies already present in contigs. Thus, the number of misassemblies may only increase in comparing to contigs, i.e. the broken version.

However, your case is probably a little bit more complicated. If your reference genome is not very close to the sequenced organism, you usually get many partially unaligned contigs (scaffolds). If such scaffold has more than 50% of unaligned bases, its misassemblies are excluded from # misassemblies as untrustworthy ones and counted in # unaligned mis. contigs metric. At the same time, the broken version may include this scaffold as a set of short contigs split by continues fragments of N's. Some of these contings may be fully unaligned while some of them may be considered as normal (less than 50% is unaligned). The misassemblies in normal contigs will be counted in # misassemblies.

To sum up, please take a look at # unaligned mis. contigs values. We suggest that the number of such contigs is higher for the scaffolded version and this is the probable source of the higher number of misassemblies in the broken assembly. You may also be interested in Icarus visualization where all unaligned mis. contigs are highlighted with grey-red color.

Q16. I evaluated multiple assemblies against the reference genome and opened Icarus Contig Alignment Viewer. Color scheme is almost self explanatory but could you explain the meaning of "similar correct contigs" (colored blue) and "similar misassembled blocks" (colored orange)? How do you define the similarity?

The algorithm is described in details in Icarus paper (see Supplementary Material, Section 1.2). The brief definition is below.

Two blocks are considered "similar" if they satisfy the following conditions altogether:

QUAST 4.6.3 manual

Contents

1. Installation

2. Running QUAST

2.1 For impatient people

2.2 Input data

2.3 GAGE mode

2.4 Command line options

2.5 Metagenomic assemblies

3. QUAST output