output the containment sequence

[yywyaoyaowu]

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]

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

Thanks! Kristen

[gbdias]

Same question here.

[ondovb]

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.