Introduction

MOTIVATION: Next-generation sequencing has become an important tool in molecular biology. Various protocols to investigate genomic, transcriptomic and epigenomic features across virtually all species and tissues have been devised. For most of these experiments, one of the first crucial steps of bioinformatic analysis is the mapping of reads to reference genomes. RESULTS: Here, we present thorough benchmarks of our read aligner segemehl in comparison with other state-of-the-art methods. Furthermore, we introduce the tool lack to rescue unmapped RNA-seq reads which works in conjunction with segemehl and many other frequently used split-read aligners. AVAILABILITY: lack is distributed together with segemehl and freely available at www.bioinf.uni-leipzig.de/Software/segemehl/.

Publications

  1. Lacking alignments? The next-generation sequencing mapper segemehl revisited.
    Cite this
    Otto C, Stadler PF, Hoffmann S, 2014-07-01 - Bioinformatics (Oxford, England)
  2. A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection.
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    Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt LM, Teupser D, Hackermüller J, Stadler PF, 2014-01-01 - Genome biology
  3. Fast and sensitive mapping of bisulfite-treated sequencing data.
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    Otto C, Stadler PF, Hoffmann S, 2012-07-01 - Bioinformatics (Oxford, England)
  4. Fast mapping of short sequences with mismatches, insertions and deletions using index structures.
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    Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J, 2009-09-01 - PLoS computational biology

Credits

  1. Christian Otto
    Developer

    Transcriptome Bioinformatics Junior Research Group, LIFE-Leipzig Research Center for Civilization Diseases, Denmark

  2. Peter F Stadler
    Developer

    Transcriptome Bioinformatics Junior Research Group, LIFE-Leipzig Research Center for Civilization Diseases, Denmark

  3. Steve Hoffmann
    Investigator

    Transcriptome Bioinformatics Junior Research Group, LIFE-Leipzig Research Center for Civilization Diseases, Denmark

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Summary
AccessionBT000039
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionDenmark
Submitted BySteve Hoffmann