This plugins contains alignment and quality control related Roddy workflows:
- PanCancer alignment workflow for whole genome (WGS) and exome (WES)
- Bisulfite core workflow (WGBS) using methylCtools
These are basically BWA alignment (bwa mem) workflows with plenty of additional quality control steps. QC-steps acting on the BAM files are mostly done through piping the input data into multiple QC tools simultaneously to achieve a high performance. All workflows can be run for each sample or with combinations of tumor- and control-samples.
Please refer to the wiki for detailed information on all aspects of the workflow, including installation, configuration structure and interpretation of results.
Your opinion matters! The development of this workflow is supported by the German Network for Bioinformatic Infrastructure (de.NBI). By completing this very short (30-60 seconds) survey you support our efforts to improve this tool.
Please see the changelogs file for details.