Christian Otto1, Peter F Stadler2, Steve Hoffmann1. 1. 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. 2. 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
Abstract
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/.
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/.
Authors: Romina Beleggia; Nooshin Omranian; Yan Holtz; Tania Gioia; Fabio Fiorani; Franca M Nigro; Nicola Pecchioni; Pasquale De Vita; Ulrich Schurr; Jacques L David; Zoran Nikoloski; Roberto Papa Journal: Int J Mol Sci Date: 2021-04-30 Impact factor: 5.923
Authors: Rolf Backofen; Fabian Amman; Fabrizio Costa; Sven Findeiß; Andreas S Richter; Peter F Stadler Journal: RNA Biol Date: 2014-04-02 Impact factor: 4.652
Authors: Deblina Patra; Mario Fasold; David Langenberger; Gerhard Steger; Ivo Grosse; Peter F Stadler Journal: Front Plant Sci Date: 2014-12-23 Impact factor: 5.753
Authors: Amine Namouchi; Marta Gómez-Muñoz; Stephan A Frye; Line Victoria Moen; Torbjørn Rognes; Tone Tønjum; Seetha V Balasingham Journal: BMC Genomics Date: 2016-10-10 Impact factor: 3.969
Authors: Carmen Aguilar; Susana Costa; Claire Maudet; R P Vivek-Ananth; Sara Zaldívar-López; Juan J Garrido; Areejit Samal; Miguel Mano; Ana Eulalio Journal: Nat Commun Date: 2021-06-07 Impact factor: 14.919