"relative_abundance" option was not provided in "contig" mode

[microjishuai]

Hi Ben,

The "contig" mode doesn't provide "relative_abundance" option for coverage measures. Could you please explain the reasons for this setting? What are your concerns about calculating the relative abundance of contigs (e.g. uncultured virus)?

Many thanks,
Shuai

[wwood]

Hi @microjishuai apologies for the slow response here.

I can't see any reason why whyat you suggest is a poor idea. You can actually achieve the same thing with a bit of hoop jumping using genome mode - specify a genome definition file where each contig is its own genome. The only other difference between the two modes is that genome mode requires 10% of the genome to be covered by 1 or more reads, otherwise it rounds the coverage (and therefore relative abundance) down to 0. You can change that using --min-covered-fraction 0.

HTH - we may add contig-wise in the future as you suggest (and to galah too, fwiw).
ben