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RWilton / Arioc

Arioc: GPU-accelerated DNA short-read alignment
BSD 3-Clause "New" or "Revised" License
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HOWTO? #3

Closed dakami closed 5 years ago

dakami commented 5 years ago

I have two fastq files for a paired WGBS read, as well as hg38.fa.

It's not clear what the sequence of operations is, to go from this, to a SAM or a BAM file. Could you assemble a quick HOWTO or a very simple cfg? For example, how do I generate gapped or ungapped seeds?

RWilton commented 5 years ago

This is documented in the Arioc user guide. Working samples for both S cerevisiae and H sapiens are provided in both the Windows and Linux downloads.