QUAST
Description
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.
License
GNU General Public License version 2.0 (GPLv2)
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of quast and load default version of quast as
module avail quast/ # list available modules module load quast # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail quast
and choose explicit version you want to use.
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
Help pages (for quast-4.6.3)
quast.py --help metaquast.py --help icarus.py --help
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
Online QUAST manual is available at http://quast.bioinf.spbau.ru/manual.html