Hello, I am trying to compare the mapping result between parabricks v4.3.2-1 and vanilla minimap2 v2.26-r1175. But I found significant different numbers of mapped reads.
Parabricks:
docker run --rm --gpus all --volume ./:/workdir --volume ./:/outputdir --workdir /workdir nvcr.io/nvidia/clara/clara-parabricks:4.3.2-1 pbrun minimap2 --preset map-ont --low-memory --ref /workdir/chr20.fa --in-fq /workdir/ulk.chr20.fq.gz --out-bam /workdir/gpu.ulk.chr20.bam
Minimap2:
minimap2 -x map-ont chr20.fa ulk.chr20.fq.gz -t32 -a | samtools view -bhS -@32 > cpu.ulk.chr20.bam
May I know why this happens and how to fix this? Thanks!
Hi @sh0rt2l0ng,
Parabricks minimap2 is compatible with minimap2 version 2.24, not 2.26 so I would compare it against that version and see if you’re facing the same issue.
You can see which version the parabricks tools are compatible with by running:
docker run --gpus all --rm nvcr.io/nvidia/clara/clara-parabricks:4.3.2-1 pbrun minimap2 --version
Please visit NVIDIA Clara - NVIDIA Docs for detailed documentation
Version Information
Tool: minimap2
pbrun: 4.3.2-1
Compatible With:
minimap2: 2.24
Thank you
with minimap v2.24-r1122
Is this related to that parabricks can not deal with ultra long reads correctly?
Hi @sh0rt2l0ng,
That might be causing an issue. Can you tell me more about the data you’re using?
Thank you
