Toward perfect reads

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