2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2020

Mikko Rautiainen, Tobias Marschall. MBG: Minimizer-based Sparse de Bruijn Graph Construction. Technical Report doi:10.1101/2020.09.18.303156v1, bioRxiv, 2020.

Download preprint: not available

Download from publisher: https://www.biorxiv.org/content/10.1101/2020.09.18.303156v1

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Bibliography entry: BibTeX


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: