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© Research
Publication : Cell systems

Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Cell systems - 14 Sep 2021

Ekim B, Berger B, Chikhi R,

Link to Pubmed [PMID] – 34525345

Link to DOI – 10.1016/j.cels.2021.08.009

Cell Syst 2021 Sep; ():

DNA sequencing data continue to progress toward longer reads with increasingly lower sequencing error rates. Here, we define an algorithmic approach, mdBG, that makes use of minimizer-space de Bruijn graphs to enable long-read genome assembly. mdBG achieves orders-of-magnitude improvement in both speed and memory usage over existing methods without compromising accuracy. A human genome is assembled in under 10 min using 8 cores and 10 GB RAM, and 60 Gbp of metagenome reads are assembled in 4 min using 1 GB RAM. In addition, we constructed a minimizer-space de Bruijn graph-based representation of 661,405 bacterial genomes, comprising 16 million nodes and 45 million edges, and successfully search it for anti-microbial resistance (AMR) genes in 12 min. We expect our advances to be essential to sequence analysis, given the rise of long-read sequencing in genomics, metagenomics, and pangenomics. Code for constructing mdBGs is freely available for download at https://github.com/ekimb/rust-mdbg/.

https://pubmed.ncbi.nlm.nih.gov/34525345