ReadXplorer - Visualization and Analysis of Mapped Sequences
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 (NGS) 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 and deletion-insertion polymorphism (SNP and DIP) detection, genomic feature and general coverage analysis. Especially for RNA-Seq data, it offers differential gene expression analysis, transcription start site (TSS) and operon detection as well as RPKM value and read count calculations. Furthermore, ReadXplorer can combine or superimpose coverage of different data sets.
Hilker, R., Stadermann, K.B., Doppmeier, D., Kalinowski, J., Stoye, J., Straube, J., Winnebald, J., Goesmann, A., (2014) ReadXplorer - Visualization and Analysis of Mapped Sequences. Bioinformatics, btu205.