Research output: Contribution to journal › Article › peer-review
metaFlye: scalable long-read metagenome assembly using repeat graphs. / Kolmogorov, Mikhail; Bickhart, Derek M. ; Behsaz, Bahar; Гуревич, Алексей Александрович; Райко, Михаил Петрович; Shin, Sung Bong ; Kuhn, Kristen ; Yuan, Jeffrey ; Polevikov, Evgeny ; Smith, Timothy P. L. ; Певзнер, Павел Аркадьевич.
In: Nature Methods, Vol. 17, No. 11, 01.11.2020, p. 1103-1110.Research output: Contribution to journal › Article › peer-review
}
TY - JOUR
T1 - metaFlye: scalable long-read metagenome assembly using repeat graphs
AU - Kolmogorov, Mikhail
AU - Bickhart, Derek M.
AU - Behsaz, Bahar
AU - Гуревич, Алексей Александрович
AU - Райко, Михаил Петрович
AU - Shin, Sung Bong
AU - Kuhn, Kristen
AU - Yuan, Jeffrey
AU - Polevikov, Evgeny
AU - Smith, Timothy P. L.
AU - Певзнер, Павел Аркадьевич
N1 - Publisher Copyright: © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.
PY - 2020/11/1
Y1 - 2020/11/1
N2 - 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.
AB - 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.
KW - HUMAN GENOME
KW - IDENTIFICATION
KW - REVEALS
UR - http://www.scopus.com/inward/record.url?scp=85092099293&partnerID=8YFLogxK
UR - https://www.mendeley.com/catalogue/b37625c6-229a-3690-8318-3ff0a8070a59/
U2 - 10.1038/s41592-020-00971-x
DO - 10.1038/s41592-020-00971-x
M3 - Article
VL - 17
SP - 1103
EP - 1110
JO - Nature Methods
JF - Nature Methods
SN - 1548-7091
IS - 11
ER -
ID: 62913419