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G-MAPSEQ – a new method for mapping reads to a reference genome

Wojciechowski P., Frohmberg W., Kierzynka M., Zurkowski P., Blazewicz J.

Foundations of Computing and Decision Sciences

2016

Vol. 41, No. 2

123--142

The problem of reads mapping to a reference genome is one of the most essential problems in modern computational biology. The most popular algorithms used to solve this problem are based on the Burrows-Wheeler transform and the FM-index. However, this causes some issues with highly mutated sequences due to a limited number of mutations allowed. G-MAPSEQ is a novel, hybrid algorithm combining two interesting methods: alignment-free sequence comparison and an ultra fast sequence alignment. The former is a fast heuristic algorithm which uses k-mer characteristics of nucleotide sequences to ﬁnd potential mapping places. The latter is a very fast GPU implementation of sequence alignment used to verify the correctness of these mapping positions. The source code of G-MAPSEQ along with other bioinformatic software is available at: http://gpualign.cs.put.poznan.pl.