Metagenomic shotgun sequence analysis- optimal approach

Question

[deni.ribicic]

Hi Folks,

I am relatively new to bioinformatics world, therefore having some issues to construct a workflow that would suit my needs. Hence, I would kindly ask for your opinion and advice. I have Illumina shotgun sequences of 5 metagenomes. I would like to end up with functional profile of all 5 samples that can be comparable. In addition, I would like to calculate taxa contribution for few genes of my interest. What would be the best approach to achieve that? Is it the right way to do the assembly and binning? Perhaps just assembly? Or use the un-assembled reads?

Regards, Deni

Answer 1

[dago]

I think it really depends on your specific questions. There could be really different approach to follow. For example, if you are interested in only specific genes then a binning would be not the ideal thing to do especially if you have complex samples as sediments or soil. You can start here:

Integrative workflows for metagenomic analysis

An introduction to the analysis of shotgun metagenomic data

Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies

Microbiome/Metagenome Analysis Workflows

But I would strongly suggest you to be more specific in your questions. Good luck!

[deni.ribicic]

Hi dago,

Thanks for the reply. Actually I am interested in specific genes (i.e. hydrocarbon degrading genes). Now if I want to calculate taxa contribution to those genes how would you do it if not binning first? What I understand is that by creating bins you are gathering potential genes belonging to the same taxon? From there you could then calculate taxa contribution for certain genes of interest?

Deni