segemehl 0.3 – Fast Short Read Mapping with Indels

segemehl 0.3


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.


the Hoffmann Junior Research Group




  • Linux





Bioinformatics. 2014 Mar 13. [Epub ahead of print]
Lacking alignments? The next generation sequencing mapper segemehl revisited.
Otto C1, Stadler PF, Hoffmann S.

Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J:
Fast mapping of short sequences with mismatches, insertions and deletions using index structures“,
PLoS Comput Biol (2009) vol. 5 (9) pp. e1000502