Cited by 717Genomics and Phylogenetic StudiesEnvironmental DNA in Biodiversity StudiesBacteriophages and microbial interactions

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MetaQUAST: evaluation of metagenome assemblies

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Mikheenko, Alla, Saveliev, Vladislav, Gurevich, Alexey·2016·Bioinformatics

DOI 10.1093/bioinformatics/btv697

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Abstract

Summary: 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.

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Authors: Mikheenko, A., Saveliev, V., & Gurevich, A.
Affiliations: St Petersburg University (RU)
Corresponding author: Gurevich, Alexey
ORCID: Mikheenko, Alla
Saveliev, Vladislav
Gurevich, Alexey
Venue: Bioinformatics
Publisher: Oxford University Press (OUP)
Published: 2015-11-26
Volume: 32
Issue: 7
Pages: 1088-1090
ISSN: 1367-4803 (ISSN-L)
1367-4811
DOI: 10.1093/bioinformatics/btv697
OpenAlex: W2175526948
Cited by: 711
References: 27
Citations by year: 2026: 76 · 2025: 100 · 2024: 104 · 2023: 92 · 2022: 78 · 2021: 82 · 2020: 57 · 2019: 44 · 2018: 34 · 2017: 34 · 2016: 9 · 2015: 1
FWCI: 11.30
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: Bioinformatics (publishedVersion)
PubMed (publishedVersion)
HighWire Press Open Archive (submittedVersion)
Funders: Russian Science Foundation (14‐50‐00069, 14-50-)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
Keywords: metagenome assembly, assembly evaluation, QUAST, assembler comparison, contig alignment
MeSH terms: Algorithms, Software, Metagenome, Metagenomics, Genomic Structural Variation

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