Display BAM quality control information for a ReadsAlignment or ReadsAlignmentSet using QualiMap.
This App runs QualiMap to produce BAM QC metrics and plots a report for an Alignment(Set).
The output report can be downloaded and includes a summary of the number of mapped reads, coverage, GC-content, mapping quality, etc. in tabular format. It also contains various plots such as PCA and coverage histograms to visualize the tabular data.
Related Publications
- Okonechnikov K, Conesa A, Garc a-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 2016;32: 292 294. doi:10.1093/bioinformatics/btv566 , https://www.ncbi.nlm.nih.gov/pubmed/26428292
App Specification:
https://github.com/kbaseapps/kb_QualiMap/tree/1efacd253aa0f3faa8e8183343f66366eccb6c7a/ui/narrative/methods/run_QualiMapModule Commit: 1efacd253aa0f3faa8e8183343f66366eccb6c7a