High-quality metagenome assembly from long accurate reads with metaMDBG
Gaëtan Benoit, Sébastien Raguideau, Robert James, Adam M. Phillippy, Rayan Chikhi, Christopher Quince
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.
Topics & Concepts
De Bruijn graphMetagenomicsDe Bruijn sequenceGenomeSequence assemblyComputational biologyPlasmidComputer scienceGraphBiologyTheoretical computer scienceGeneticsGeneMathematicsCombinatoricsGene expressionTranscriptomeGenomics and Phylogenetic StudiesBacteriophages and microbial interactionsPlant Virus Research Studies