Quality Assessment Tool for Genome Assemblies by CAB

About

Short intro
Further reading
How to cite
Brief project history
Authors
Funding
License and Terms of use

Short intro

QUAST evaluates genome assemblies by computing various metrics, including

.. and builds convenient plots for different metrics

QUAST can work with and without a reference genome, though the output is considerably smaller in the latter case. The pipeline relies on multiple open-source tools, including minimap2, GlimmerHMM, and BUSCO.

Further reading

More details are on the project page and in Gurevich et al., Bioinformatics, 2013.
You may also want to check out the Help page with a step-by-step tutorial on using this website and interpreting its output.
Thorough metric descriptions are available in the online manual. A nice illustrated explanation of N50 and similar metrics by Elin Videvall (with assistance from the QUAST team) is here.
Finally, we invite you to read all QUAST publications listed below to understand the algorithms behind the tool and its applicability to various domains.

Don’t hesitate to contact us if you still have any questions!

How to cite

If you have found QUAST useful in your research, please cite:

Versatile genome assembly evaluation with QUAST-LG
Alla Mikheenko, Andrey Prjibelski, Vladislav Saveliev, Dmitry Antipov, Alexey Gurevich
Bioinformatics (2018) DOI: 10.1093/bioinformatics/bty266

Icarus: visualizer for de novo assembly evaluation
Alla Mikheenko, Gleb Valin, Andrey Prjibelski, Vladislav Saveliev, Alexey Gurevich
Bioinformatics (2016) DOI: 10.1093/bioinformatics/btw379

MetaQUAST: evaluation of metagenome assemblies
Alla Mikheenko, Vladislav Saveliev, Alexey Gurevich
Bioinformatics (2016) DOI: 10.1093/bioinformatics/btv697

QUAST: quality assessment tool for genome assemblies
Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi and Glenn Tesler
Bioinformatics (2013) DOI: 10.1093/bioinformatics/btt086

Brief project history

2011, July — project start
2012, August 14 — first public release at SourceForge (QUAST v.1.0.0)
2012, September 27 — theweb server first launch (at http://quast.bioinf.spbau.ru/, shut down in January 2020)
2013, February 19 — the first QUAST publication was out in Bioinformatics
2013, April 15 — Prof. Steven Salzberg recommended QUAST at Faculty Opinions (former F1000)
2015, July 13 — the QUAST repository was opened for public access on GitHub, the tool became fully open sourced
2018, November 2 — the total number of QUAST downloads exceeded 100,000 (bioconda & SourceForge)
2020, April 4 — the web server relauched at its current location
2021, August 31CZI acknowledged QUAST as an essential software tool for biomedicine and supported with a grant (jointly with SPAdes)

Authors

Core developers (in alphabetical order):
Alexey Gurevich (since 2011)
Alla Mikheenko (since 2015)
Vlad Saveliev (2012-2017)

Also contributed (in alphabetical order):
Dmitry Antipov
Aleksey Komissarov
Andrey Prjibelski
Glenn Tesler
Gleb Valin
Irina Vasilinetc
Nikolay Vyahhi
.. and dozens of QUAST users who provided their feedback

Logo design by Elena Strelnikova

Funding

Over the years, the QUAST development was supported by many funding agencies/sources:

The server is running using computational resources provided by the Computer Center of Research park of St. Petersburg State University.

License and Terms of use

QUAST is licensed under GPL v2 and it is free to use for everybody; there is no login requirement for the web server. However, some of build-in third-party tools are not under GPL v2. See LICENSE for details. In particular, the GeneMark gene prediction software has a stricter license, so it is not included in the web server pipeline, but can be used with the command-line version if you are eligible.

Liability: the QUAST webserver is developed and maintained in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

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