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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Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts
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Hidden Resistome: Enrichment Reveals the Presence of Clinically Relevant Antibiotic Resistance Determinants in Treated Wastewater-Irrigated Soils
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Terabase-scale metagenome coassembly with MetaHipMer
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Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system
Overholt, W. A., Hölzer, M., Geesink, P., Diezel, C., Marz, M., & Küsel, K. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15186 · Cited by 72
Challenges and opportunities in sharing microbiome data and analyses
Huttenhower, C., Finn, R. D., & McHardy, A. C. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01484-x · Cited by 74
“Benchmarking software, data and platforms AMBER 80 , OPAL 81 , CAMI platform 43 , LEMMI 82 , MetaQuast 83 , CAMISIM 84 , curatedMetagenomicData 58 Processed data figshare, Dryad, Zenodo, OSF, the Harvard Dataverse , PANGAEA, MGnify (MAGs) Few repositories allow pre-analysed microbiome data…”
Method
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Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit
Meyer, F., Lesker, T.-R., Koslicki, D., Fritz, A., Gurevich, A. A., Darling, A. E., Sczyrba, A., Bremges, A., & McHardy, A. C. (2021) · Nature Protocols · doi:10.1038/s41596-020-00480-3 · Cited by 74
“Evaluation metrics are extensively tested and implemented in the MetaQUAST 23 , AMBER 24 , and OPAL 25 benchmarking packages (Table 3), available via Bioconda 26 .”
MethodSelf-citation
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Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic
Klapper, M., Hübner, A., Ibrahim, A., Wasmuth, I., Borry, M., Haensch, V. G., Zhang, S., Al‐Jammal, W. K., Suma, H. R., Yates, J. A. F., et al. (2023) · Science · doi:10.1126/science.adf5300 · Cited by 67
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Buddle, S., Forrest, L., Akinsuyi, N., Bernal, L. M. M., Brooks, T., Venturini, C., Miller, C. M., Brown, J. R., Storey, N., Atkinson, L., et al. (2024) · Genome Medicine · doi:10.1186/s13073-024-01380-x · Cited by 70
“The assembly of the resulting contigs (> 150nt only) was assessed using metaQUAST [82].”
Method
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Goethem, M. W. V., Osborn, A. R., Bowen, B. P., Andeer, P. F., Swenson, T. L., Clum, A., Riley, R. W., He, G., Koriabine, M., Sandor, L., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-02809-4 · Cited by 62
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The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes
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“The number of contigs, contig length, GC content, N50, and L50 assembly statistics were calculated with metaQUAST (Mikheenko et al., 2016; Supplementary Table 2).”
Method
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Functional Strain Redundancy and Persistent Phage Infection in Swiss Hard Cheese Starter Cultures
Somerville, V., Berthoud, H., Schmidt, R. S., Bachmann, H.-P., Meng, Y. H., Fuchsmann, P., von Ah, U., & Engel, P. (2022) · The ISME Journal · doi:10.1038/s41396-021-01071-0 · Cited by 55
TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats
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Self-citation
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“2 [66] after which we identified open reading (ORFs) using Prodigal v2.”
Method
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Jouffret, V., Miotello, G., Culotta, K., Ayrault, S., Pible, O., & Armengaud, J. (2021) · Microbiome · doi:10.1186/s40168-021-01139-1 · Cited by 52
Poultry manure-derived microorganisms as a reservoir and source of antibiotic resistance genes transferred to soil autochthonous microorganisms
Męcik, M., Buta, M., Paukszto, Ł., Maździarz, M. A., Wolak, I., Harnisz, M., & Korzeniewska, E. (2023) · Journal of Environmental Management · doi:10.1016/j.jenvman.2023.119303 · Cited by 52
MetaPhage: an Automated Pipeline for Analyzing, Annotating, and Classifying Bacteriophages in Metagenomics Sequencing Data
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“Finally, the last part of the report provides general statistics about read quality check/preprocessing and assembly metrics (calculated using the metaQuast tool [18]).”
Method
Inherent tendency of Synechococcus and heterotrophic bacteria for mutualism on long-term coexistence despite environmental interference
Nair, S., Zhang, Z., Li, H., Zhao, H., Shen, H., Kao, S., Jiao, N., & Zhang, Y. (2022) · Science Advances · doi:10.1126/sciadv.abf4792 · Cited by 51
De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding
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Metagenomic surveillance of antibiotic resistome in influent and effluent of wastewater treatment plants located on the Qinghai-Tibetan Plateau
Shi, B., Zhao, R., Su, G., Liu, B., Liu, W., Xu, J. F., Li, Q., & Meng, J. (2023) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2023.162031 · Cited by 51
Phables: from fragmented assemblies to high-quality bacteriophage genomes
Mallawaarachchi, V., Roach, M. J., Decewicz, P., Papudeshi, B. N., Giles, S. K., Grigson, S. R., Bouras, G. S., Hesse, R. D., Inglis, L. K., Hutton, A. L. K., et al. (2023) · Bioinformatics · doi:10.1093/bioinformatics/btad586 · Cited by 49
“We evaluated the resolved phage genomes using metaQUAST (Mikheenko et al. 2016).”
Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungi
Meiser, A., Otte, J., Schmitt, I., & Grande, F. D. (2017) · Scientific Reports · doi:10.1038/s41598-017-14576-6 · Cited by 51
The Earth BioGenome project: opportunities and challenges for plant genomics and conservation
Expósito‐Alonso, M., Drost, H., Burbano, H. A., & Weigel, D. (2019) · The Plant Journal · doi:10.1111/tpj.14631 · Cited by 47

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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MetaQUAST: evaluation of metagenome assemblies

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