metagenomics dataset and assembly

Question

[Petchimuthu]

I have a basic doubt about metagenomic datasets. I have downloaded datasets from bioproject PRJNA398089 into 3 categories: control, Crohn's sample, and ulcerative colitis. So, I need to preprocess this. Should I divide my analysis work into three categories and compare them? or can I assemble for the entire data set?

Answer 1

[JC]

Considering an initial hypothesis regarding variation in species between the samples, the individual assembly per sample is preferred.