Please mention in details the advantage and disadvantage of any particular software if you recommend. Thanks in advance.
There are numerous software available for Metagenomics ,each having a fair share of advantages and disadvantages. It is much better to use combination of tools rather than emphasizing upon a single tool. QIIME and Mothur are quite good for metagenomics and metatranscriptomics. For beginners its much better to start from SilvaNGS or MG-RAST. For extensive statistical analysis one can use METAGENAssist. Galaxy also provide many incorporated tools , and one can easily design his/her workflow.One can also use MetagenomeSeq (Bioconductor).
Hope this helps
Regards
Pankaj
There are numerous software available for Metagenomics ,each having a fair share of advantages and disadvantages. It is much better to use combination of tools rather than emphasizing upon a single tool. QIIME and Mothur are quite good for metagenomics and metatranscriptomics. For beginners its much better to start from SilvaNGS or MG-RAST. For extensive statistical analysis one can use METAGENAssist. Galaxy also provide many incorporated tools , and one can easily design his/her workflow.One can also use MetagenomeSeq (Bioconductor).
Hope this helps
Regards
Pankaj
I would also add that it is important to understand that different types of questions lead to different tools to be used.
Are you interested in comparing communities, identifying link between microbiome composition and a trait, or find functions, etc.?
MEGAN (now at version 6) has a great collection of tools for microbiome data. It is widely used. However, I don't have a complete comparison of MEGAN vs. other tools like QIIME mentioned earlier.
http://ab.inf.uni-tuebingen.de/software/megan6/
- Badges
- Science method