Citation

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

Hoffmann, S., Otto, C., Kurtz, S., Sharma, C. M., Khaitovich, P., Vogel, J., Stadler, P. F., & Hackermüller, J. (2009). Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Computational Biology, 5(9), e1000502. https://doi.org/10.1371/journal.pcbi.1000502

Hoffmann, S., Otto, C., Doose, G., Tanzer, A., Langenberger, D., Christ, S., Kunz, M., Holdt, L. M., Teupser, D., Hackermüller, J., & Stadler, P. F. (2014). A multi-split mapping algorithm for circular RNA, splicing, trans-splicing, and fusion detection. Genome Biology, 15(2), R34. https://doi.org/10.1186/gb-2014-15-2-r34

For the Bisulfite option:

Otto, C., Stadler, P. F., & Hoffmann, S. (2012). Fast and sensitive mapping of bisulfite-treated sequencing data. Bioinformatics, 28(13), 1698-1704. https://doi.org/10.1093/bioinformatics/bts254