Metagenomics Analysis Pipeline

Question

[vishalchanda364]

Hi there, I am new to metagenomics analysis and I am doing a virome analysis from the sample, can anyone help me suggesting the best tool to assemble my metagenomics data and to remove the contigs <1Kb size? plus if anyone can suggest me some best pipeline to got forward which i can incorporate in my raw data pre-processing.?

[Asaf]

Take a look at flow-craft project, it was built mainly for metagenome analysis. It's an easy way to try out some tools and generate pipelines on the fly.

[vishalchanda364]

Thank you so much Asaf. I will look through it and incorporate any of the steps which I have missed.

Answer 1

[onestop_data]

Here is a pipeline done to target viromes [paper]. If you need to do ORF calling, here is a tool which was defined for viral datasets paper