MetaQUAST: evaluation of metagenome assemblies
Open accessAbstract
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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Whole genomes of organisms, in addition to strain tracking, can be extracted from shotgun metagenomic data, allowing for evolutionary analysis of specific organisms associated with a particular disease or environment.
“Whole genomes of organisms, in addition to strain tracking, can be extracted from the data, allowing for evolutionary analysis of specific organisms associated with a particular disease or environment.79, 80, 81”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [79]
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- Authors
- Mikheenko, A., Saveliev, V., & Gurevich, A.
- Affiliations
- St Petersburg University (RU)
- Corresponding author
- 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
- 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
- Physical Sciences › Environmental Science › Ecology › 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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