G-MAPSEQ – a new method for mapping reads to a reference genome
[ 1 ] Instytut Informatyki, Wydział Informatyki, Politechnika Poznańska | [ P ] pracownik
2016
artykuł naukowy
angielski
- computational biology
- next generation sequencing
- parallel computing
- reads mapping
EN The problem of reads mapping to a reference genome is one of themost essential problems in modern computational biology. The most popular algo-rithms used to solve this problem are based on the Burrows-Wheeler transform andthe FM-index. However, this causes some issues with highly mutated sequences dueto a limited number of mutations allowed. G-MAPSEQ is a novel, hybrid algorithmcombining two interesting methods: alignment-free sequence comparison and an ultrafast sequence alignment. The former is a fast heuristic algorithm which usesk-mercharacteristics of nucleotide sequences to find potential mapping places. The latteris a very fast GPU implementation of sequence alignment used to verify the correct-ness of these mapping positions. The source code of G-MAPSEQ along with otherbioinformatic software is available at: http://gpualign.cs.put.poznan.pl.
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