marbl/Mash

output the containment sequence

Opened this issue · 3 comments

yywyaoyaowu commented

Hi
mash screen is very friendly and quick. I use it to test if my assembly is containment with bacterium. Can it output which contig is containmented? I want to remove the containment contig.
I don't need to blast to nr database if it can output the containment contig. blast is very slow. Thanks very much!

Yaoyao

kdc10 commented

I have the same inquiry. @yywyaoyaowu, were you able to find a way to do this?

Thanks!
Kristen

gbdias commented

Same question here.

ondovb commented

Unfortunately screen does not keep track of this. There could be a command line option to make hash counts specific to each contig. The tradeoff would be that a contaminant split across multiple contigs would only appear as partly contained in each of those contigs, and the similarity would be underestimated. Output could also explode with combinations of queries and contigs.