ReduceReads parallelism

aihardin

I'm working with ReduceReads and would like to use it in some kind of parallel mode. The presentation mentions that a 50x way run may drastically reduce run time but I'm not sure how to invoke this. I tried -nt and it complained. Should I be giving it multiple intervals and merging? If so, how does it deal with edge variants?

Thanks.

Carneiro

Yes, you need to run non overlapping (farther than read length apart) intervals independently and merge the results together.

-nt is incompatible with Read Walkers, unfortunately.