Segemehl

Description

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 supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.

Environment Modules

Run module spider segemehl to find out what environment modules are available for this application.

Environment Variables

• HPC_SEGEMEHL_DIR - installation directory
• HPC_SEGEMEHL_BIN - executable directory

Citation

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

Categories

biology, ngs, sequencing