Metagenomic Analysis

Question

[beatrice.aren]

Hi,

I am trying to do binning on some metagenomic data. Can anyone recommend a beginner friendly binning program? I would prefer if after binning, I can export the sequences belonging to a bacterium of interest for BLAST so that I can search for gene homology for that particular bacterium.

Answer 1

[Khader Shameer]

Here is a great article to start with: read section on binning. I would recommend end-to-end solutions like MG-RAST / Metagenassist / Clovr for metagenomic analysis

Answer 2

[Manu Prestat]

If you want to start with your own blast results, I would deeply recommend MEGAN. If BLAST is too slow, they also do provide a blastx alternative called PAUDA ; MEGAN lets you load the blast(-like) query fasta file along with the blast(-like) result which allows you to export sequences corresponding to whatever bin you choose (your bacterium of interest for instance). MG-RAST is a wonderful tool, it provides all kinds of visualization, taxonomic and functional analyses, a bunch of cross-refs... but it has a critical drawback: the similarity search strategy from which all results are derived is tweaked to let the argonne server analyze all those data from all over the world at the cost of sensitivity. An other alternative, less user-friendly and slower than MG-RAST is IMG/M.