metagenomic analysis pipelines for gene prediction, annotation and functional analysis.

Question

[faizansaleem1992]

Hello,

I have used mg-rast pipeline for metagenomic analysis of my data. but I want to use some other pipelines too for gene prediction and functional analysis. kindly suggest some names and tutorial if possible.

Thank you.

Answer 1

[f.a.galkin]

I am also looking for functional profiling software atm and I have come across MOCAT2 and NGLess But these seem rather heavy weight, as they require an assembly stage.

I wonder if there are any light weight options for functional analysis. Maybe just blasting each read would be more sensible.

If you have come around any notable packages, please share them here.

[Luispedro]

Author of NGLess here (also MOCAT2, but that is no longer maintained, using it is not recommended).

Depending on which environment you are working on, NGLess may not require assembly. If there are already gene catalogs for the environment at hand, you can use them. Otherwise, yes, assembly is recommended.

Feel free to ask more detailed questions on the ngless mailing-list:

https://groups.google.com/d/forum/ngless

I generally would say that blasting each read is not a good practice nowadays: the reads are just too short. Even if you don't use our tools, I'd still ask you to not do it that way.

Answer 2

[Lakshman Teja]

Just try metawrap @https://github.com/bxlab/metaWRAP