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DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data
GNU General Public License v3.0
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HLA*ASM #101

Closed bsb2014 closed 11 months ago

bsb2014 commented 1 year ago

I am wondering if you have a plan to update HLA*ASM. Is it possible to replace nucmer with minimap2 for alignment? Thanks!

AlexanderDilthey commented 11 months ago

Hi @bsb2014, we have no immediate plans to update HLA*ASM.

However, note that the script already supports minimap2 alignment - activated via parameter use_minimap2, activated e.g. like so: --use_minimap2 1.