Can I use the bowtie index file in the subdirectory 'reference'

[JingAnyaSun]

Hi Sebastian,

Thanks for creating the package!
I'm a bit confused on the bowtie index files required, do I have to do the index file using bowtie by myself or I can directly use the 'reference' folder in the subdirectory under seq2HLA?

I look forward to your reply.

Best,
Jing