PanCancer alignment workflow

The alignment workflow produces aligned BAM files from FASTQ files using the BWA aligner. The default settings of the workflow are implemented like in the ICGC PanCancer workflow. The pipeline also produces a rich set of quality values as well as coverage plots. Supported are the alignment and quality control of whole genome, whole exome and whole genome bisulfite sequencing data, including tagmentation-WGBS. For WGBS data, methylations are called with methylCtools ( The workflow is implemented with Roddy.


This email address is being protected from spambots. You need JavaScript enabled to view it.

Funding: Continuing development, support, and maintenance partially funded by de.NBI