The DOI matches its Crossref record; 47 of the 47 references it cites were found in a registry or an index.
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Open accessAbstract
Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of "marker" genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.
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“Quality and completeness were assessed using CheckM (completeness > 94% required) [24].”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [24]
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“The genome completeness is 100% based on a comparison with cyanobacterial marker genes using checkM analysis 19.”
From The Draft Genome of a Hydrogen-producing Cyanobacterium, Arthrospira platensis NIES-46 (2019) · cites this paper as [19]
In the citing paper
“The success of such binning procedures is validated by investigating the number of single-copy core-genome genes within each bin, as implemented by software such as CheckM (Parks et al., 2015).”
From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Parks et al., 2015
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Pfam: the protein families database
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FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
Price, M. N., Dehal, P. S., & Arkin, A. P. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp077 · Cited by 5,602
McDonald, D. T., Price, M. N., Goodrich, J. K., Nawrocki, E. P., DeSantis, T. Z., Probst, A. J., Andersen, G. L., Knight, R. D., & Hugenholtz, P. (2011) · The ISME Journal · doi:10.1038/ismej.2011.139 · Cited by 5,144
Self-citationYang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960
Whelan, S., & Goldman, N. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003851 · Cited by 2,849
Community structure and metabolism through reconstruction of microbial genomes from the environment
Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F. (2004) · Nature · doi:10.1038/nature02340 · Cited by 2,417
Self-citationInsights into the phylogeny and coding potential of microbial dark matter
Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J.-F., Darling, A., Malfatti, S., Swan, B. K., Gies, E. A., et al. (2013) · Nature · doi:10.1038/nature12352 · Cited by 2,394
Self-citationDendroPy: a Python library for phylogenetic computing
Sukumaran, J., & Holder, M. T. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq228 · Cited by 1,637
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Wu, Q., Li, W., Kwok, L.-Y., Lv, H., Sun, J., & Sun, Z. (2024) · Food Research International · doi:10.1016/j.foodres.2024.114840 · Cited by 9
Inskeep, W. P., Jay, Z. J., McKay, L. J., & Dlakić, M. (2025) · Nature Communications · doi:10.1038/s41467-024-55079-z · Cited by 9
Degradation of polyethylene by three bacteria isolated from coastal beach
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Di Pierro, F., Sagheddu, V., Galletti, S., Casaroli, A., Labrini, E., Soldi, S., Cazzaniga, M., Bertuccioli, A., Matera, M., Cavecchia, I., et al. (2026) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-025-10522-5 · Cited by 5
Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort
Mudhluli, T. E., Kujawska, M., Mueller, J., Felsl, A., Truppel, B.-A., Hall, L. J., Chitsike, I., Gomo, E., & Zhou, D. T. (2024) · BMC Genomics · doi:10.1186/s12864-024-10618-2 · Cited by 3
Fu, P., Qi, H., & Liu, W. (2025) · Foods · doi:10.3390/foods14152747 · Cited by 3
Di Pierro, F., Zerbinati, N., Guasti, L., Cazzaniga, M., Bertuccioli, A., Palazzi, C. M., Labrini, E., Sagheddu, V., & Soldi, S. (2024) · Microbiology Resource Announcements · doi:10.1128/mra.00580-24 · Cited by 2
Metadata
- Authors
- Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W.
- Affiliations
- The University of Queensland (AU)
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2015-05-14
- Volume
- 25
- Issue
- 7
- Pages
- 1043-1055
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- PMC
- PMC4484387
- OpenAlex
- W2112364185
- Cited by
- 12,496
- References
- 47
- Citations by year
- 2026: 1931 · 2025: 2112 · 2024: 1929 · 2023: 1587 · 2022: 1403 · 2021: 1204 · 2020: 928 · 2019: 582 · 2018: 381 · 2017: 261 · 2016: 117 · 2015: 47
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- Natural Sciences and Engineering Research Council of Canada
- Great Barrier Reef Foundation
- Australian Research Council (DP120103498, DP1093175)
- Discovery Outstanding Researcher Award
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Health Sciences › Medicine › Microbiology (medical) › Bacterial Identification and Susceptibility Testing
- Keywords
- CheckM, genome completeness, genome contamination, draft genome sequence, microbial genomes, marker genes, single-cell genomics, metagenome, genome quality assessment, bacterial and archaeal genomes
- MeSH terms
- Metagenome, Metagenomics, Genome, Microbial
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