search

ngless-toolkit / ng-meta-profiler

Profiler for metagenomics based on NGLess
https://ngless.embl.de
12 stars 2 forks source link

Profiler for Soil metagenomes #3

Open EorgeKit opened 11 months ago

EorgeKit commented 11 months ago

Hello @luispedro @unode

What's the recommendation when dealing with soil metagenomes since there is no particular predefined profiler for it or any other metagenome that has no predefined profiler for that matter?

luispedro commented 11 months ago

Hi @EorgeKit,

For soil in particular, I would really recommend going through the assembly+MAG building route (i.e., a de novo approach) rather than profiling against existing databases.

EorgeKit commented 11 months ago

Thanks @luispedro t seems as though ngless is not customized for denovo , or I am missing something?

luispedro commented 11 months ago

Yes, there is more support for reference-based approaches, but you can assemble too.

You can ask more open ended questions at

https://groups.google.com/g/ngless