parallelGWAS

Motivation: Next-generation sequencing platforms enable the rapid generation of large-scale sequencing data from non-model organisms at a reasonable cost. The identification of sequence homology to a known species often provides the first clues about the function of a newly sequenced gene. However, performing homology searches is time consuming, resulting in a computational bottleneck. Results: Here, I introduce a novel tool—Frog—that identifies exact matches of sequences by using a backward search with the Burrows–Wheeler Transform (BWT). It identifies homologous regions to the query sequence by using BLAST extension. Frog drastically reduced CPU time compared with existing methods. It was found that Frog could detect homology between short reads and a reference sequence. It was also found to be much faster than BLAST and BWA. Frog promises to be a useful tool for fast genomic sequence analysis; however, further technical refinement may be necessary.