QUAST
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Application data |
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| Created by | Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler |
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| Biological application domain(s) | Sequence assembly, Data handling |
| Principal bioinformatics method(s) | Visualisation, Sequence assembly validation |
| Technology | Any |
| Created at | Academic University, St. Petersburg, Russia |
| Maintained? | Yes |
| Input format(s) | FASTA, Fasta.gz, GFF3, GFF, TXT |
| Output format(s) | Delimited Text, Plain text, PDF, LaTeX, Graphics (png), HTML |
| Software features | Data Visualisation, Assembly Quality Evaluation, Detailed Reports |
| Programming language(s) | Python, C, Perl |
| Software libraries | Biopython, MatPlotLib |
| Licence | GPLv2 |
| Operating system(s) | Linux, Mac OS X |
| Contact: | gurevich@bioinf.spbau.ru |
Summary: QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports.
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Description
QUAST evaluates genome assemblies by computing various metrics:
- N50, length of the shortest contig from all that cover 50% of all assembly
- NG50, where the reference genome is being covered
- NA50 and NGA50, where aligned blocks instead of contigs are taken
- misassemblies, misassembled and unaligned contigs or contigs bases
- genes and operons covered
- and other metrics
It also builds convenient plots for different metrics
- cumulative contigs length
- all kinds of N-metrics
- genes and operons covered
- GC content
Source code is available at http://sourceforge.net/p/quast/
Web-server and examples of QUAST reports are presented at http://quast.bioinf.spbau.ru/
Links
References
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