Hello all, I'm working with some folks in central africa who have been sequencing BDBV outbreak and have been using viralrecon to analyse their TWIST data and I've been asked to weigh in, I've never used viralrecon since I have my own pipes for the amplicon and metagenomic aspects of it Does anyone have a more informed opinion on the suitability of the pipe for such datasets? I've got vague memories that PCR deduplication is desirable for TWIST I think somebody recommended @Joon Klaps viralmetagenome pipe previously?

probe capture experiments like twist can introduce huge number of pcr duplicates due to the two rounds of pcr amp. The first is post barcoding, it's standard in any illumina experiment (usually ~6 rounds), the second is post hybridisation capture. For twist is ~15 rounds of PCR amp. For Agilent Magnus it's like 21 rounds. So yes, dedup is super important.