The DOI matches its Crossref record; 27 of the 27 references it cites were found in a registry or an index.
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 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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Self-citationBLAST+: architecture and applications
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metaSPAdes: a new versatile metagenomic assembler
Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. (2017) · Genome Research · doi:10.1101/gr.213959.116 · Cited by 4,496
Using SPAdes De Novo Assembler
Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., & Korobeynikov, A. (2020) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.102 · Cited by 3,555
Versatile genome assembly evaluation with QUAST-LG
Mikheenko, A., Prjibelski, A. D., Saveliev, V., Antipov, D., & Gurevich, A. A. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty266 · Cited by 1,537
Self-citationCharacterization of the gut microbiome using 16S or shotgun metagenomics
Jovel, J., Patterson, J., Wang, W., Hotte, N., O'Keefe, S., Mitchel, T., Perry, T., Kao, D., Mason, A. L., Madsen, K. L., et al. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00459 · Cited by 942
“Sequences that surpass a dissimilarity threshold (bit-score) are progressively placed on higher taxonomy levels.”
BackgroundMethodA practical guide to amplicon and metagenomic analysis of microbiome data
Liu, Y., Qin, Y., Chen, T., Lu, M., Qian, X., Guo, X., & Bai, Y. (2020) · Protein & Cell · doi:10.1007/s13238-020-00724-8 · Cited by 931
Metadata
- 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
- 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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