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Maps short sequencer reads to reference genomes. Segemehl is a read aligner that allows to detect mismatches, insertions and deletions. The software implements a matching strategy based on enhanced suffix arrays (ESA): it aims to find the best-scoring seed for each suffix of a read. The tool lack, which rescues unmapped RNAseq, reads and works in conjunction with segemehl and many other frequently used split-read aligners, is distributed together with it.

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Segemehl classification

Segemehl specifications

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Segemehl distribution


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Segemehl support



  • Steve Hoffmann <>


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Transcriptome Bioinformatics Junior Research Group, LIFE-Leipzig Research Center for Civilization Diseases, Interdisciplinary Center for Bioinformatics, Bioinformatics Group, Department of Computer Science, University Leipzig, RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; Santa Fe Institute, Santa Fe, NM, USA; Department of Theoretical Chemistry, University of Vienna, Austria; Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany; Center for non-coding RNA in Technology and Health, University of Copenhagen, Denmark

Funding source(s)

Supported by LIFE and BMBF through ICGC MMML-Seq (01KU1002J). LIFE—Leipzig Research Center for Civilization Diseases, Universitat Leipzig, funded by means of the European Union, by the European Regional Development Fund (ERDF) and by means of the Free State of Saxony.

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