Question: Should I Be Using K-Mer Coverage In Velvet Parameters Instead Of Nucleotide Coverage?
gravatar for Panos
9.5 years ago by
Geneva, Switzerland
Panos1.7k 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 • 4.6k views
ADD COMMENTlink written 9.5 years ago by Panos1.7k
gravatar for Jeremy Leipzig
9.5 years ago by
Philadelphia, PA
Jeremy Leipzig19k 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 9.5 years ago by Jeremy Leipzig19k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2093 users visited in the last hour