MBG: Minimizer-based sparse de Bruijn Graph construction.

Abstract

MotivationDe Bruijn graphs can be constructed from short reads efficiently and have been used for many purposes. Traditionally, long-read sequencing technologies have had too high error rates for de Bruijn graph-based methods. Recently, HiFi reads have provided a combination of long-read length and low error rate, which enables de Bruijn graphs to be used with HiFi reads.ResultsWe have implemented MBG, a tool for building sparse de Bruijn graphs from HiFi reads. MBG outperforms existing tools for building dense de Bruijn graphs and can build a graph of 50× coverage whole human genome HiFi reads in four hours on a single core. MBG also assembles the bacterial E.coli genome into a single contig in 8 s.Availability and implementationPackage manager: https://anaconda.org/bioconda/mbg and source code: https://github.com/maickrau/MBG.Supplementary informationSupplementary data are available at Bioinformatics online.