ReadXplorer - Visualization and Analysis of Mapped Sequences

[-tron!c-]

Hello everybody,

I'd like to introduce the open-source software ReadXplorer developed during my PhD. It combines visualization and automatic analysis of read mapping data received from any mapping tool. It is specifically designed to deal with multiple mapped reads and therefore classifies the reads again during import into the software.

ReadXplorer is implemented in Java 1.8, so it runs on all major OS.

The publication is available here: http://bioinformatics.oxfordjournals...0/16/2247.long

The software is freely available here: http://www.readxplorer.org (goto "Access/Download" to download) and has an integrated help as well as a manual available on the homepage.

Please note that it is inevitable to assure that the reference name (locus) is identical in the reference files and the mapping files. Otherwise ReadXplorer cannot associate a mapping to the corresponding reference sequence (e.g. chromosome).

Main features:

Visualizations:
- Reference
- Coverage
- Alignments
- Read Pairs
- Data set combination
- Result tables for analyses

Analyses:
- SNP and DIP detection
- Differential Gene Expression Analysis (requires R and uses DESeq, DESeq2 and baySeq)
- Transcription Start Site (TSS) Detection
- Read Count and Normalization Claculation (RPKM and TPM)
- Operon Detection
- Genome Rearrangement Detection (using GASV)
- Feature Coverage Analysis
- Coverage Analysis
- Correlation Analysis

I hope some of you find the software useful.
Of course you are welcome to comment, make suggestions for improvements and report bugs.