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segemehl website  

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 mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.

Required Modules


  • segemehl

System Variables

  • HPC_SEGEMEHL_DIR - installation directory


If you publish research that uses segemehl you have to cite it as follows:

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

Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt L, Teupser D, Hackermueller J, Stadler PF: "A multi-split mapping algorithm for circular RNA, splicing, trans-splicing, and fusion detection", Genome Biology (2014) 15:R34

For the Bisulfite option:

Otto C, Stadler PF, Hoffmann S: "Fast and sensitive mapping of bisulfite-treated sequencing data", Bioinformatics (2012) 28:1698-1704


  • Validated 4/5/2018