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Old 04-19-2013, 06:03 AM   #5
Gorbenzer
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Location: italy

Join Date: Apr 2012
Posts: 45
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Quote:
Originally Posted by rhinoceros View Post
Something like MG-RAST? Or more like local stuff? tRNAscan, FragGeneScan, standalone blast, blat, MEGAN, mothur, etc.. it really depends on what you plan to study..
Local would be great, we have two servers for our analysis.

I'd like to try all the different approaces:
- Try to assembly all the data to see if i can get draft genomes of a few highly present species;
- Try to assembly all the data, predict ORFs and annotate them to obtain the gene pool of the sample;
- Try to "annotate" all the single reads to find out what genes are higly represented in the sample.

I would love to try gene prediction and annotation (including GO, EC and pathway prediction if possible) softwares specific for metagenomic analysis.

Thx for the help!
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