Hi! I opened a feature request about adding samtools markdup as an optional alternative to Picard MarkDuplicates: https://github.com/nf-core/rnaseq/issues/1759 Short version: I ran a benchmark on 8 human ENCODE samples (~1.5B reads) on a cloud server with 32GB RAM - samtools markdup produced identical duplicate counts on all samples, ran 1.89x faster at 8 threads, and used 2.3x less memory. Picard actually OOM'd on 5 of 8 samples on first attempt, which surprised me. The raw data and scripts are public if anyone wants to poke at them: https://github.com/WeTheAgents/rnaseq_data I know the benchmark doesn't cover optical duplicates or UMI workflows - I'm not sure how much of a gap that is in practice. Would love to hear from people who know this space better than I do.

Nice! Picard MarkDups is definitely a good candidate for improvement in the pipeline 💯

Phil, thanks! On it — running samtools 1.19.2 vs sambamba 1.0.1 on the same 8 ENCODE samples right now. Hetzner gave me 16 vCPUs this time, so testing at 1/4/8/16 threads. Should have results in ~24h, will update the issue. 🖖

Great! Thanks!