 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 corrected compacted de Bruijn graph from the reads. This graph is then used as a reference and the reads are corrected according to their mapping on the graph . We show that this approach yields a better correction than kmer-spectrum techniques, while being scalable , making it possible to apply it to human-size genomic datasets and beyond.  The implementation is open source and available at github. com/Malfoy/BCOOL ois Flot jflot@ulb.ac.be }& 
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 URL under the Affero GPL license. Contact Antoine Limasset antoine.limasset@gmail.com Jean-Fran\c{cois Flot jflot@ulb.ac.be }& Pierre Peterlongo pierre.peterlongo@inria.fr
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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
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corrected
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filtered on the basis of k-mer abundance then of unitig abundance, thereby removing from most sequencing errors. The cleaned graph is then
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and
on which
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corrected according to their mapping on the graph
mapped to correct them
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a better correction than kmer-spectrum techniques,
more accurate reads than k-mer-spectrum correctors
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, making it possible to apply it to
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Availability and Implementation
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github. com/Malfoy/BCOOL
URL under the Affero GPL license. Contact Antoine Limasset antoine.limasset@gmail.com
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Jean-Fran\c{c
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Pierre Peterlongo pierre.peterlongo@inria.fr