FANGS: High Speed Sequence Mapping for Next Generation Sequencers

Date Added: Mar 2010
Format: PDF

Next Generation Sequencing machines are generating millions of short DNA sequences (reads) everyday. There is a need for efficient algorithms to map these sequences to the reference genome to identify SNPs or rare transcripts and to fulfill the dream of personalized medicine. The authors present a Fast Algorithm for Next Generation Sequencers (FANGS), which dynamically reduces the search space by using q-gram filtering and pigeon hole principle to rapidly map 454-Roche reads onto a reference genome. FANGS is a sequential algorithm designed to find all the matches of a query sequence in the reference genome tolerating a large number of mismatches or insertions/deletions.