pFANGS: Parallel High Speed Sequence Mapping for Next Generation 454-Roche Sequencing Reads

Abstract—Millions of DNA sequences (reads) are generated by Next Generation Sequencing machines everyday. There is a need for high performance algorithms to map these sequences to the reference genome to identify single nucleotide polymorphisms or rare transcripts to fulfill the dream of per-sonalized medicine. In this paper, we present a high-throughput parallel sequence mapping program pFANGS. pFANGS is designed to find all the matches of a query sequence in the reference genome tolerating a large number of mismatches or insertions/deletions. pFANGS partitions the computational workload and data among all the processes and employs load-balancing mechanisms to ensure better process efficiency. Our experiments show that, with 512 processors, we are able to map approximately 31 million 454/Roche queries of length 500 each to a reference human genome per hour allowing 5 mismatches or insertion/deletions at full sensitivity. We also report and compare the performance results of two alternative parallel implementations of pFANGS: a shared memory OpenMP implementation and a MPI-OpenMP hybrid implementation. Keywords-sequence mapping; next generation sequencers; 454 sequencers; parallel computing I