and produces several reports:
- for all contigs and all input genomes merged into one,
- separate reports for only contigs aligned to a particular genome,
- for the contigs not aligned to any reference provided.
Usage:
metaquast.py contigs_1 contigs_2 ... -R reference_1,reference_2,reference_3,...
All other options for metaquast.py are the same as for quast.py.
2. MetaGeneMark is used to find genes in metagenomic assemblies.
In metaquast.py by default, in quast.py with --meta option.
3. In place of --allow-ambiguity, a new option --ambiguity-usage (-a) is introduced.
The new option lets specify a way to process ambiguous regions:
-a one, -a all or -a none.
4. A new option --labels (or -l) allows to provide human-readable assembly names.
Those names will be used in reports, plots and logs, instead of file names.
For example:
-l SPAdes,IDBA-UD
if your labels include spaces, use quotes:
-l "SPAdes 2.5, SPAdes 2.4, IDBA-UD"
-l SPAdes,"Assembly 2",Assembly3
5. Minor improvements of HTML reports.
6. Fixed bugs in misassemblies detection algorithm.
2.1 Option --strict-NA is added to control computation of NAx/NGAx metrics.
This option forces QUAST to break contigs by any misassembly event,
including local misassemblies (like in v.2.0). By default, QUAST v.2.1
breaks contigs only by extensive misassemblies to compute NAx/NGAx
(like in v.1.*).
Improvement of indels computation. QUAST now counts consecutive single nucleotide
indels as one indel. Total length of all indels is also reported (equal to
indels metric evaluated with previous versions). Short (<= 5 bp) and long (>5 bp)
indels are reported.
Option --est-ref-size is added to set estimated reference size for computing NGx
metrics in case a reference genome is not available.
GAGE mode is parallelized.
Fixed bugs in misassemblies detection algorithm.
Fixed bugs in SNPs detection algorithm.
Fixed bugs in processing circular chromosomes (affects Genome fraction, genes,
operons).
Fixed several minor bugs.