Title: 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 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-François Flot jflot@ulb.ac.be &
Pierre Peterlongo pierre.peterlongo@inria.fr