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Alignment and Quality Control Plugin for Roddy

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

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.

Change Logs

Please see the changelogs file for details.