segemehl v0_1_3 (Map short reads to known genome with tolerance for mismatches and indels using suffix arrays for high accuracy matching)
segemehl is software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to map primer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA).