Short read error correction using an FM-index

Whole genome sequencing is becoming more affordable, but sequencing errors complicate the analysis and diminish the utility of the data. We present FMRC, a new tool for correcting errors in DNA short reads from high-throughput sequencing. It uses a Burrows-Wheeler Transform and FM-index to enable a k-mer counting approach for correcting substitution, insertion, and deletion errors. In general, it corrects errors more effectively than other error correction tools, leading to better alignments and de novo assemblies. FMRC is freely available at https://github.com/sgreenstein/fmrc.