This plugins contains alignment and quality control related Roddy workflows:

• PanCancer alignment workflow for
  • whole genome sequencing (WGS) and
  • whole exome sequencing (WES)
• Whole genome bisulfite workflow (WGBS) using methylCtools. For tagmentation WGBS and PBAT a modified version is used (described here).

These workflows 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 minimize I/O and thus maximize throughput.

Please see the changelogs file for details.