I have sequences from 2 separate extractions for the same individual. We are working on a highly polymorphic region, and only want to keep reads that are found in both fastq files (from separate Illumina lanes). I've already paired the sequences if that changes anything.
The ideal tool would match sequences from two separate fastq (or fasta files if that's the input), and output only the matching sequences. I thought BBMap might have something, but I couldn't find anything appropriate.
I've also looked at jMHC, even though I'm not using MHC data, but I'm struggling to even install that on the computing cluster.