Segemehl is a 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). Segemehl now supports the SAM format, reads gzip’ed queries to save both disk and
memory space and allows bisulfite sequencing mapping and split read mapping.
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