Sampling 10X dataset when having extreme coverage
I have a question regarding extreme coverage and how I can deal with it to do several assemblies with supernova.
We got 200X on a genome project assembly, a coverage largely higher than the recommended 56X in your guidance. I was wondering if I can subsample my dataset to get several assemblies and therefore the most infomation from it.
But your doc did not recommend to use --bcfrac option as it is deprecated and give worse results than using raw data. I understood that using --maxreads help to achieve a good assembly regarding the recommended 56X coverage. And I cannot use --accept-extreme-coverage because my dataset is 1,2x10^13 reads, much higher thant the supernova limit 2,14x10^9 reads.
Did supernova subsample different reads if I run it several times with the same --maxreads limit?
Is there a way to tell supernova to subsample different reads for the same amount of reads?
Re: Sampling 10X dataset when having extreme coverage
I've forwarded your email to our support team and they will be reaching out to you directly, as there may be a bit of back and forth to help answer your question.