I just thought it would be worthwhile posting this , as it would be beneficial for those who are stepping into field of metagenomics . Below are the compiled list of tools and links to a few of them, that can be used for primary and secondary analysis of metagenomic sequence data.(Though there are plenty missed out here..)
Please do add to this list, as the list will be ever growing...:)
May I add a plug for http://www.ebi.ac.uk/metagenomics? We have developed a pipeline for taxonomic and functional analysis of metagenomic samples and we also archive your raw sequence data in the SRA on your behalf. We're always looking for suggestions of how to improve our service, so please contact us with feedback. We will be launching new features on our website later next month and hope to publish the resource in NAR database issue this year.
Cool new profiler tool for metagenomic data, ShortBRED.
ShortBRED is a pipeline to take a set of protein sequences, group them into families, extract a set of distinctive strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.
They manage a curated list of bioinformatics tools.
From their site: "OMICtools strives to accelerate research in bioinformatics, making tools accessible to everyone and offering a stimulating work environment to assist life scientists extracting new findings from the omics data."
I tried DocMind Analyst on the AWS cloud and found it very convenient and easy to use. It works with a graphical user interface and uses mothur and RDP for read processing and classification. Their tutorials are also very good for beginners.