MBG：基于最小化器的稀疏德布鲁因图构建。
MBG: Minimizer-based sparse de Bruijn Graph construction.
作者信息
Rautiainen Mikko, Marschall Tobias
机构信息
Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.
Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.
出版信息
Bioinformatics. 2021 Aug 25;37(16):2476-2478. doi: 10.1093/bioinformatics/btab004.
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 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 IMPLEMENTATION
Package manager: https://anaconda.org/bioconda/mbg and source code: https://github.com/maickrau/MBG.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
德布鲁因图可以从短读段高效构建，并已用于多种目的。传统上，长读长测序技术的错误率过高，不适用于基于德布鲁因图的方法。最近，高保真读段提供了长读长和低错误率的组合，这使得德布鲁因图能够与高保真读段一起使用。
结果
我们实现了MBG，一种用于从高保真读段构建稀疏德布鲁因图的工具。MBG优于现有的用于构建密集德布鲁因图的工具，并且可以在单核上4小时内构建覆盖度为50倍的整个人类基因组高保真读段的图。MBG还能在8秒内将细菌大肠杆菌基因组组装成一个单重叠群。
可用性和实现方式
包管理器：https://anaconda.org/bioconda/mbg，源代码：https://github.com/maickrau/MBG。
补充信息
补充数据可在《生物信息学》在线获取。
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