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

Bioinformatics
Antoine LimassetPierre Peterlongo

Abstract

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. 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. The implementation is open source, available at http://github.com/Malfoy/BCOOL under the Affero GPL license and as a Bioconda package. Supplementary data are available at Bioinformatics online.

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Citations

Nov 15, 2019·F1000Research·Luis YanesBernardo J Clavijo
Sep 18, 2020·BMC Bioinformatics·Nicola PrezzaGiovanna Rosone
Aug 21, 2020·Bioinformatics·Felix KallenbornBertil Schmidt
Jan 10, 2021·Genome Biology·Guillaume HolleyBjarni V Halldorsson
Jun 4, 2021·BMC Bioinformatics·Xuan ZhangJinyan Li

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