ReadXplorer

https://www.uni-giessen.de/fbz/fb08/Inst/bioinformatik/software/ReadXplorer

Methods

linear single view single scale single focus segregated no abstraction no arrangement no interconnection segment sparse type point contiguous type

Tool

Access Format standalone app
Supported Files sambamcram fasta other
License GPL
Tool name

ReadXplorer
Tool Link http://www.readxplorer.org
Documentation https://www.uni-giessen.de/fbz/fb08/Inst/bioinformatik/software/ReadXplorer/documentation

Paper

ReadXplorer--visualization and analysis of mapped sequences.

Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, et al. ReadXplorer—visualization and analysis of mapped sequences. Bioinformatics. Oxford University Press; 2014;30: 2247–2254.

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.