Hi Tosin,

The selection of tool for metagenomics depends upon the computational resources available to you. There are plethora of tools which can you use :

Server based:

MG-RAST:http://www.mg-rast.org/

Gaia: https://metagenomics.sequentiabiotech.com/

SilvaNGS: https://www.arb-silva.de/

Galaxy platform :https://usegalaxy.org/

Kaiju: http://kaiju.binf.ku.dk/server

Standalone:

Mothur

QIIME

I hope this helps.

Best Wishes

Pankaj

If you want to do everything, Quality check, assembly, annotations, Diversity etc QIIME is the best. For only taxonomic diversity MOTHUR is enough. Both the software run on LINUX platform.

Qiime (http://qiime.org/) or MOTHUR .

Thank you so much Pankaj Kumar Singh . I would check them out.

Aww thank you Sahar Abdelrazek

Thank you V.J Rejish Kumar

Squuezemeta pipeline (https://github.com/jtamames/SqueezeMeta)