DeBGR: an efficient and near-exact representation of the weighted de Bruijn graph.

ABSTRACT:

Motivation

Almost all de novo short-read genome and transcriptome assemblers start by building a representation of the de Bruijn Graph of the reads they are given as input. Even when other approaches are used for subsequent assembly (e.g. when one is using 'long read' technologies like those offered by PacBio or Oxford Nanopore), efficient k -mer processing is still crucial for accurate assembly, and state-of-the-art long-read error-correction methods use de Bruijn Graphs. Because of the centrality of de Bruijn Graphs, researchers have proposed numerous methods for representing de Bruijn Graphs compactly. Some of these proposals sacrifice accuracy to save space. Further, none of these methods store abundance information, i.e. the number of times that each k -mer occurs, which is ke

SUBMITTER: Pandey P 

PROVIDER: S-EPMC5870571 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature