ReadXplorer—visualization and analysis of mapped sequences

Rolf Hilker, Kai Bernd Stadermann, Daniel Doppmeier, Jörn Kalinowski, Jens Stoye, Jasmin Straube, Jörn Winnebald, Alexander Goesmann
2014 Bioinformatics  
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
more » ... nd 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 opensource software at http://www.readxplorer.org along with a detailed manual.
doi:10.1093/bioinformatics/btu205 pmid:24790157 pmcid:PMC4217279 fatcat:i6o7gvzc7zbmvn4cg3nbnwlvke