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Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs
- Source :
- Bioinformatics 36(5) 1374-1381 (2020)
- Publication Year :
- 2017
-
Abstract
- Motivations 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 data sets or consider reads as mere suites of k-mers, without taking into account their full-length read 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 st ep, 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 from 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 and available at http://github.com/Malfoy/BCOOL under the Affero GPL license. Contact Antoine Limasset antoine.limasset@gmail.com & Jean-Fran\c{c}ois Flot jflot@ulb.ac.be & Pierre Peterlongo pierre.peterlongo@inria.fr<br />Comment: RECOMB SEQ 2018 Submission
Details
- Database :
- arXiv
- Journal :
- Bioinformatics 36(5) 1374-1381 (2020)
- Publication Type :
- Report
- Accession number :
- edsarx.1711.03336
- Document Type :
- Working Paper
- Full Text :
- https://doi.org/10.1093/bioinformatics/btz102