HLA typing on Nanopore and PacBio reads

Open kokyriakidis opened this issue 4 years ago • 3 comments

Hello @lkuchenb ,

I wanted to ask if this tool can handle fastq reads from Nanopore or PacBio. With a different aligner I can run xHLA and HLA-LA. My question is mostly about Optitype. Will it be able to handle long reads?

Mar 20 '21 09:03 kokyriakidis

@kokyriakidis Just a small question: how did you get xHLA to work on Nanopore fastq's? We're having some trouble currently. Did you use minimap2? Which reference did you use, Hg38 no alt contigs?

Apr 12 '22 11:04 BioinformaNicks

@BioinformaNicks Try to use hg38-noalt and minimap2.

Apr 12 '22 17:04 kokyriakidis

@kokyriakidis Firstly, thanks a lot! Second, we're using that, but still having some issues on public data. Any particular processing you used? Running their Docker image without any modifications?

Apr 13 '22 07:04 BioinformaNicks