Fig. 2

The different modules of Je (green squared blocks) and their usage in workflows. The clip, demultiplex and demulitplex-illu are the three possible entry points to process barcoded fastq files (blue squared blocks). In most setups (plain arrows), clipped or demultiplexed fastq files are mapped to the genome (grey squared block) using your favorite mapper and filtered for duplicate reads by the Je’s markdupes module using extracted UMIs. In more complex barcoding designs (e.g. composite barcodes, Supplementary Text), additional clipping before or after the sample demultiplexing step could be required (dashed arrows)