Question: Should I Be Using K-Mer Coverage In Velvet Parameters Instead Of Nucleotide Coverage?
3
gravatar for Panos
7.6 years ago by
Panos1.6k
Geneva, Switzerland
Panos1.6k wrote:

Is Velvet using k-mer coverage values instead of nucleotide coverage in its parameters?

Suppose, for example, that my average read length is 36bp and k-mer size is 21. If I want to eliminate all regions with coverage of 2x or below should I use '-covcutoff 2' or '-covcutoff 0.9' (the latter based on a formula in the Velvet manual which converts nucleotide coverage to k-mer coverage - see Section 5.1 in the manual)? What about the '-exp_cov' parameter? Should I use k-mer coverage values for this parameter, too?

assembly coverage velvet • 3.9k views
ADD COMMENTlink written 7.6 years ago by Panos1.6k
3
gravatar for Jeremy Leipzig
7.6 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

yes 0.9, everything is kmer-coverage (read kmers per contig kmers), my understanding is that nothing is Velvet is x-coverage based, including exp-cov

ADD COMMENTlink written 7.6 years ago by Jeremy Leipzig18k
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