articleNature BiotechnologyJan 2, 2024HYBRID OA

High-quality metagenome assembly from long accurate reads with metaMDBG

GBGaëtan BenoitSRSébastien RaguideauRJRobert JamesAMAdam M. PhillippyRCRayan Chikhi

Norwich Research Park · Earlham Institute · +6 more institutions

PubMed
Indexed incrossrefpubmed

Abstract

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.

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Topics & keywords

Topics
Keywords
  • De Bruijn graph
  • Metagenomics
  • De Bruijn sequence
  • Genome
  • Sequence assembly
  • Computational biology
  • Plasmid
  • Computer science
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