I'd like to demultiplex and deduplicate reads using in-line barcodes from read2 and UMIs from the read1 and read2. The format is like this (read2 is a short read, containing only barcode and UMI).
1: UMI-primer-READ 2: barcode-UMI
UMI-tools seems to be suitable, but I failed to find how to sort based on UMI combinations. Maybe you know of a tool that can handle both UMIs and barcodes, and can sort reads based on combinations of UMIs from both PE reads?
Any help with where to start with that highly appreciated...