The DOI matches its Crossref record; 84 of the 84 references it cites were found in a registry or an index.
metaFlye: scalable long-read metagenome assembly using repeat graphs
Open accessAbstract
Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. Finally, we show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products. Long-read metagenomics offers a valuable approach for profiling bacterial communities. This work presents a long-read assembler, metaFlye, that specifically addresses the challenges of assembling metagenomes.
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Towards population-scale long-read sequencing
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Self-citationComputational methods for chromosome-scale haplotype reconstruction
Garg, S. (2021) · Genome Biology · doi:10.1186/s13059-021-02328-9 · Cited by 116
Duller, S., Vrbancic, S., Szydłowski, Ł., Mahnert, A., Blohs, M., Predl, M., Kumpitsch, C., Zrim, V., Högenauer, C., Kosciolek, T., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52037-7 · Cited by 21
Metadata
- Authors
- Kolmogorov, M., Bickhart, D. M., Behsaz, B., Gurevich, A., Rayko, M., Shin, S. B., Kuhn, K., Yuan, J., Polevikov, E., Smith, T. P. L., & Pevzner, P. A.
- Venue
- Nature Methods
- Published
- 2020-10-05
- Volume
- 17
- Issue
- 11
- Pages
- 1103-1110
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W3091506611
- Cited by
- 1,077
- References
- 84
- FWCI
- 28.56
- Type
- journal article
- Language
- en
- Open access
- green
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- Kolmogorov, M., Bickhart, D. M., Behsaz, B., Gurevich, A., Rayko, M., Shin, S. B., Kuhn, K., Yuan, J., Polevikov, E., Smith, T. P. L., & Pevzner, P. A. (2020). metaFlye: scalable long-read metagenome assembly using repeat graphs. Nature Methods. https://doi.org/10.1038/s41592-020-00971-x
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