Closed liangjinsong closed 5 years ago
Dear @liangjinsong,
I am happy to hear that you find our resource useful! :)
Regarding your questions:
mash screen
does not provide this information. The containment analysis is done by processing the input data as a whole, i.e. the presence of k-mers is checked for the complete sample and not for each input sequence separately. If you have long read data or contigs I would suggest that you download the PLSDB data, and perform a local analysis using mash sketch -i
and mash dist
. The -i
option will allow you to to create sketches for each input sequence and you can then compare each of them to the reference sequences. I plan to add this option to PLSDB in the next update; until then, this kind of analysis has to be done locally.Dear VGalata, Thank you very much for your detailed response! My questions are now completely solved. Thanks again~
Excited to see the PLSDB you developed, because it helps with what I an doing. I want to identify the plasmid contigs in metagenomic assemblies using the Mash screen command in my local server. I feel that the default parameter of Min. identity (0.99) in Mash screen is much higher than that used in other similarity analysis. I ask for help on two issues below.
Thanks~