Pacbio workflow

Hi, I’m wondering if/when Parabricks will have support for GPU-accelerated analysis of long-read HiFi data from PacBio. I saw a post in a technical blog here advertising that a long-read genomics workflow would be available with the 4.1 release of Parabricks, but I haven’t been able to find long-read-specific GPU-accelerated tools such as Minimap2. Thanks!

Hellow @rlinder02,

In this latest version of Parabricks 4.2.1, we now have a minimap workflow. Please note that these will only work with PacBio data. You can find the full workflow here.

Hi @gburnett,

Thanks so much for posting this! I will definitely be giving this a try. Is there a way to specify just having the GPU-accelerated version of minimap2 run and output aligned bams without subsequently running deepvariant? Thanks!

Yes, if you just run this minimap, then it will give you a BAM and you can do whatever you want with it after that.