PerM

PerM (Periodic Seed Mapping) is a mapping software designed to efficiently map large next-generation sequencing data, specifically for ABI's sequencer (SOLiD system) that encodes sequence data into color signals. It uses periodic spaced seeds to improve mapping efficiency for large reference genomes compared to other state-of-the-art programs. PerM requires only 4.5 bytes per base to index the human genome, allowing entire genomes to be loaded to memory while multiple processors simultaneously map reads to the reference. The software offers full sensitivity for up to three mismatches and high sensitivity for four and five mismatches while minimizing the number of random hits per query.