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Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

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 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 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
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Contributor : Pierre Peterlongo Connect in order to contact the contributor
Submitted on : Thursday, December 12, 2019 - 2:06:41 PM
Last modification on : Tuesday, January 4, 2022 - 6:14:20 AM
Long-term archiving on: : Friday, March 13, 2020 - 9:50:02 PM


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Antoine Limasset, Jean-François Flot, Pierre Peterlongo. Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. Bioinformatics, Oxford University Press (OUP), 2019, ⟨10.1093/bioinformatics/btz102⟩. ⟨hal-02407243⟩



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