MBG: Minimizer-based Sparse de Bruijn Graph Construction [article]

Mikko Rautiainen, Tobias Marschall
2020 bioRxiv   pre-print
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
more » ... building dense de Bruijn graphs, and can build a graph of 50x 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 seconds.AvailabilityPackage manager: https://anaconda.org/bioconda/mbg and source code: https://github.com/maickrau/MBG
doi:10.1101/2020.09.18.303156 fatcat:gipx44vcurestaqmgxifgqybxi