High-quality metagenome assembly from long accurate reads with metaMDBG.

Autor: Benoit G; Organisms and Ecosystems, Earlham Institute, Norwich, UK., Raguideau S; Organisms and Ecosystems, Earlham Institute, Norwich, UK., James R; Gut Microbes and Health, Quadram Institute, Norwich, UK., Phillippy AM; Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA., Chikhi R; Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Paris, France., Quince C; Organisms and Ecosystems, Earlham Institute, Norwich, UK. christopher.quince@earlham.ac.uk.; Gut Microbes and Health, Quadram Institute, Norwich, UK. christopher.quince@earlham.ac.uk.; School of Biological Sciences, University of East Anglia, Norwich, UK. christopher.quince@earlham.ac.uk.; Warwick Medical School, University of Warwick, Coventry, UK. christopher.quince@earlham.ac.uk.
Jazyk: angličtina
Zdroj: Nature biotechnology [Nat Biotechnol] 2024 Sep; Vol. 42 (9), pp. 1378-1383. Date of Electronic Publication: 2024 Jan 02.
DOI: 10.1038/s41587-023-01983-6
Abstrakt: 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.
(© 2024. The Author(s).)
Databáze: MEDLINE
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