title: Lacking alignments? The next-generation sequencing mapper segemehl revisited.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  lack is distributed together with segemehl and freely available at www.bioinf.uni-leipzig.de/Software/segemehl/.
authors.affiliation: 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, New Mexico, USA, Department of Theoretical Chemistry, University of Vienna, Austria, Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany and Center for non-coding RNA in Technology and Health, University of Copenhagen, DenmarkTranscriptome 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, New Mexico, USA, Department of Theoretical Chemistry, University of Vienna, Austria, Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany and Center for non-coding RNA in Technology and Health, University of Copenhagen, Denmark.
authors.forename: Christian
authors.initials: C
authors.lastname: Otto
authors.affiliation: 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, New Mexico, USA, Department of Theoretical Chemistry, University of Vienna, Austria, Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany and Center for non-coding RNA in Technology and Health, University of Copenhagen, DenmarkTranscriptome 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, New Mexico, USA, Department of Theoretical Chemistry, University of Vienna, Austria, Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany and Center for non-coding RNA in Technology and Health, University of Copenhagen, DenmarkTranscriptome 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, New Mexico, USA, Department of Theoretical Chemistry, University of Vienna, Austria, Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany and Center for non-coding RNA in Technology and Health, University of Copenhagen, DenmarkTranscriptome 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, Fra
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.affiliation: 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, New Mexico, USA, Department of Theoretical Chemistry, University of Vienna, Austria, Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany and Center for non-coding RNA in Technology and Health, University of Copenhagen, DenmarkTranscriptome 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, New Mexico, USA, Department of Theoretical Chemistry, University of Vienna, Austria, Max-Planck-Institute for Mathematics in Sciences, Leipzig, Germany and Center for non-coding RNA in Technology and Health, University of Copenhagen, Denmark.
authors.forename: Steve
authors.initials: S
authors.lastname: Hoffmann
mesh_terms: D000465:Algorithms; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012313:RNA / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software
chemical_list: D012313:RNA