Pandey P, Bender MA, Johnson R, Patro R. deBGR: an efficient and near-exact representation of the weighted de Bruijn graph.
Bioinformatics 2017;
33:i133-i141. [PMID:
28881995 PMCID:
PMC5870571 DOI:
10.1093/bioinformatics/btx261]
[Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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 key in transcriptome assemblers.
RESULTS
We present a method for compactly representing the weighted de Bruijn Graph (i.e. with abundance information) with essentially no errors. Our representation yields zero errors while increasing the space requirements by less than 18-28% compared to the approximate de Bruijn graph representation in Squeakr. Our technique is based on a simple invariant that all weighted de Bruijn Graphs must satisfy, and hence is likely to be of general interest and applicable in most weighted de Bruijn Graph-based systems.
AVAILABILITY AND IMPLEMENTATION
https://github.com/splatlab/debgr .
CONTACT
rob.patro@cs.stonybrook.edu.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
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