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MBG: Minimizer-based Sparse de Bruijn Graph Construction
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Motivation
De 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.
Results
We 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 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.
Availability
Package manager:
https://anaconda.org/bioconda/mbg
and source code:
https://github.com/maickrau/MBG
Title: MBG: Minimizer-based Sparse de Bruijn Graph Construction
Description:
Motivation
De 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.
Results
We 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 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.
Availability
Package manager:
https://anaconda.
org/bioconda/mbg
and source code:
https://github.
com/maickrau/MBG.
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