QUAST

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Popis

QUAST performs fast and convenient quality evaluation and comparison of genome assemblies.

QUAST computes a number of well-known metrics, including contig accuracy, number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper andin the manual). A comprehensive analysis results in summary tables (in plain text, tab-separated and LaTeX formats) and colorful plots. The tool also produces web-based reports condensing all information in one easy to navigate file.

QUAST has an intuitive command-line interface and a detailed manual to help users run it and understand its output.

Availability

Version 2.3 is available for all users of MetaCentrum.

Use

Load module:

module add quast-2.3

Run the application by command quast.py, e.g

quast.py test_data/contigs_1.fasta \
         test_data/contigs_2.fasta \
         -R test_data/reference.fasta.gz \
         -G test_data/genes.txt \
         -O test_data/operons.txt \
         --threads 4

You can find files used in the example above at sourceforge.net/projects/quast/ For appropriate use of parallelization is important to set the parameter threads, which specified number of used computational threads. It is set to the number of CPU cores implicitly. Favourable solution is use for this purpose the variable which represents number of reserved CPU cores:

--threads $PBS_NUM_PPN

Documentation

On-line documentation you can find on http://quast.bioinf.spbau.ru/manual.html

Licence

GNU General Public License version 2.0 (GPLv2)

Program manager

meta@cesnet.cz

Homepage

http://bioinf.spbau.ru/quast