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Bioinformatics. 2016 Apr 1;32(7):1088-90. doi: 10.1093/bioinformatics/btv697. Epub 2015 Nov 26.

MetaQUAST: evaluation of metagenome assemblies.

Author information

1
Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg 199034, Russia.

Abstract

During the past years we have witnessed the rapid development of new metagenome assembly methods. Although there are many benchmark utilities designed for single-genome assemblies, there is no well-recognized evaluation and comparison tool for metagenomic-specific analogues. In this article, we present MetaQUAST, a modification of QUAST, the state-of-the-art tool for genome assembly evaluation based on alignment of contigs to a reference. MetaQUAST addresses such metagenome datasets features as (i) unknown species content by detecting and downloading reference sequences, (ii) huge diversity by giving comprehensive reports for multiple genomes and (iii) presence of highly relative species by detecting chimeric contigs. We demonstrate MetaQUAST performance by comparing several leading assemblers on one simulated and two real datasets.

AVAILABILITY AND IMPLEMENTATION:

http://bioinf.spbau.ru/metaquast

CONTACT:

aleksey.gurevich@spbu.ru

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26614127
DOI:
10.1093/bioinformatics/btv697
[Indexed for MEDLINE]

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