The alignment workflow produces aligned bam files from fastq files. The user can choose between different versions of bwa. The default settings of the workflow are implemented after the ICGC PanCancer workflow. The pipeline also produces a rich set of quality values as well as coverage plots for each genome individually and combined ones if a tumor normal pair is processed.
Homepage
https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows
Documentation
https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows/wiki