High-quality metagenome assembly from long accurate reads with metaMDBG

被引：20

作者：

Benoit, Gaetan ^{[1
]}

Raguideau, Sebastien ^{[1
]}

James, Robert ^{[2
]}

Phillippy, Adam M. ^{[3
]}

Chikhi, Rayan ^{[4
]}

Quince, Christopher ^{[1
,2
,5
,6
]}

机构：

[1] Earlham Inst, Organisms & Ecosyst, Norwich, England

[2] Quadram Inst, Gut Microbes & Hlth, Norwich, England

[3] NHGRI, Genome Informat Sect, Bethesda, MD USA

[4] Inst Pasteur, Dept Computat Biol, Sequence Bioinformat, Paris, France

[5] Univ East Anglia, Sch Biol Sci, Norwich, England

[6] Univ Warwick, Warwick Med Sch, Coventry, England

来源：

NATURE BIOTECHNOLOGY | 2024年 / 42卷 / 09期

基金：

英国生物技术与生命科学研究理事会; 英国医学研究理事会; 英国科研创新办公室; 英国自然环境研究理事会; 美国国家卫生研究院;

关键词：

D O I：

10.1038/s41587-023-01983-6

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over sequences of minimizers to address variations in genome coverage depth and an abundance-based filtering strategy to simplify strain complexity. For complex communities, we obtained up to twice as many high-quality circularized prokaryotic metagenome-assembled genomes as existing methods and had better recovery of viruses and plasmids. An assembler considering variable coverage depths increases the number of near-complete metagenome-assembled genomes.

引用

页码：1378 / 1383

页数：20

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