ReadXplorer--visualization and analysis of mapped sequences

Rolf Hilker; Kai Bernd Stadermann; Daniel Doppmeier; Jörn Kalinowski; Jens Stoye; Jasmin Straube; Jörn Winnebald; Alexander Goesmann

doi:10.1093/bioinformatics/btu205

ReadXplorer--visualization and analysis of mapped sequences

Bioinformatics. 2014 Aug 15;30(16):2247-54. doi: 10.1093/bioinformatics/btu205. Epub 2014 Apr 30.

Authors

Rolf Hilker¹, Kai Bernd Stadermann², Daniel Doppmeier¹, Jörn Kalinowski¹, Jens Stoye², Jasmin Straube¹, Jörn Winnebald¹, Alexander Goesmann¹

Affiliations

¹ Institute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, Germany.
² Institute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, GermanyInstitute of Medical Microbiology, Justus-Liebig-University, 35392 Giessen, Germany, Faculty of Biology, Institute for Bioinformatics, Center for Biotechnology, Computational Genomics, Center for Biotechnology, Technology Platform Genomics, Center for Biotechnology, Genome Informatics, Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany and Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, 35392 Giessen, Germany.

Abstract

Motivation: Fast algorithms and well-arranged visualizations are required for the comprehensive analysis of the ever-growing size of genomic and transcriptomic next-generation sequencing data.

Results: ReadXplorer is a software offering straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. A unique specialty of ReadXplorer is the quality classification of the read mappings. It is incorporated in all analysis functions and displayed in ReadXplorer's various synchronized data viewers for (i) the reference sequence, its base coverage as (ii) normalizable plot and (iii) histogram, (iv) read alignments and (v) read pairs. ReadXplorer's analysis capability covers RNA secondary structure prediction, single nucleotide polymorphism and deletion-insertion polymorphism detection, genomic feature and general coverage analysis. Especially for RNA-Seq data, it offers differential gene expression analysis, transcription start site and operon detection as well as RPKM value and read count calculations. Furthermore, ReadXplorer can combine or superimpose coverage of different datasets.

Availability and implementation: ReadXplorer is available as open-source software at http://www.readxplorer.org along with a detailed manual.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computer Graphics
Gene Expression Profiling
Genomics / methods
High-Throughput Nucleotide Sequencing / methods*
Operon
Polymorphism, Genetic
Polymorphism, Single Nucleotide
RNA / chemistry
Sequence Alignment / methods*
Sequence Analysis, DNA / methods*
Software*
Transcription Initiation Site

Substances

RNA