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.
Looks like this is a different FANTOM. The first FANTOM is a functional and taxonomic analysis of metagenomes. In contrast, the other one is FANTOM (Functional ANnoTation Of the Mammalian genome) in the fields of transcriptome analysis. Please correct me if I was mistaken.
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.
You seem to be advertising docmind analytics. I'd recommend you create a Tool type post and explain this tool, including its pricing strategy. The website is confusing on what is free and what their pricing system is. Please do not bulk-add answers recommending this tool.
Thanks for your comment, Ram. I am not affiliated with the company but I know the owner. So I guess I have a conflict of interest. However, I really like his idea and software, particularly for non-expert in computer science (I consider myself as such). That's why I am positive about it. I have forwarded your recommendation regarding a tool type post and publishing a clear pricing policy.
At the moment it works only for 16S rRNA sequencing. But soon shotgun metagenomics analysis will be implemented. I will submit a little overview over all its functions soon in the tool section.
It seems that many links did not work anymore. Maybe some updates will help. Thanks.
This an awesome list!
Galaxy is convenient
Hi,
I am working on Metagenomics data. I am trying to predict promoters after assembly. I would appreciate if someone can suggest any good tool.
Thanks
Ali
Can you share some mature analysis pipeline to solve the most common metagenomic questions?
Thanks Vijay, you shared several different metagenome assembly? which one is the most welcomed?
Hi Vijay, Some collection to toxic genes/transcript from all the metagenomics references?