Figure 2. Diagram of different processing and library-merging points based on the nature of different libraries.

Merge points represent merging of related BAM files as defined by metadata fields in an input TSV file. ‘colchem’ refers to the colour chemistry system of Illumina sequencers (2 for e.g., NextSeq or 4 for HiSeq machines). ‘PE/SE’ refers to paired-end and single-end sequencing chemistries. ‘UDG’ refers to uracil DNA glycosylase treatment, a laboratory procedure to completely or partially remove C to T miscoding lesions. Lane refers to sequencing lane.