HLA typing on Nanopore and PacBio reads

[kokyriakidis]

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?

[BioinformaNicks]

@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?

[kokyriakidis]

@BioinformaNicks Try to use hg38-noalt and minimap2.

[BioinformaNicks]

@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?