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- Title
Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs.
- Authors
Limasset, Antoine; Flot, Jean-François; Peterlongo, Pierre
- Abstract
Motivation Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large datasets or consider reads as mere suites of k -mers, without taking into account their full-length sequence information. Results We propose a new method to correct short reads using de Bruijn graphs and implement it as a tool called Bcool. As a first step, Bcool constructs a compacted de Bruijn graph from the reads. This graph is filtered on the basis of k -mer abundance then of unitig abundance, thereby removing most sequencing errors. The cleaned graph is then used as a reference on which the reads are mapped to correct them. We show that this approach yields more accurate reads than k -mer-spectrum correctors while being scalable to human-size genomic datasets and beyond. Availability and implementation The implementation is open source, available at http://github.com/Malfoy/BCOOL under the Affero GPL license and as a Bioconda package. Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects
DE Bruijn graph
- Publication
Bioinformatics, 2020, Vol 36, Issue 5, p1374
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btz102