metaFlye: scalable long-read metagenome assembly using repeat graphs.
Journal
Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604
Informations de publication
Date de publication:
11 2020
11 2020
Historique:
received:
16
07
2020
accepted:
07
09
2020
revised:
22
08
2020
pubmed:
7
10
2020
medline:
26
1
2021
entrez:
6
10
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 33020656
doi: 10.1038/s41592-020-00971-x
pii: 10.1038/s41592-020-00971-x
pmc: PMC10699202
mid: NIHMS1627039
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1103-1110Subventions
Organisme : NIGMS NIH HHS
ID : P41 GM103484
Pays : United States
Organisme : NHGRI NIH HHS
ID : R25 HG011022
Pays : United States
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