Tag Archives: QIIME

Video Tip of the Week: MetaPhlAn and Galaxy

CPB Using Galaxy 2 from Galaxy Project on Vimeo.

for loading and using datatypes and  the OpenHelix Galaxy tutorial for getting familiar with Galaxy interface and usage.

Metagenomics analysis can be a bit daunting at times, but there are a good number of tools out there to assist a researcher in analysis.  Integrated Microbial Genomes at JGI has some excellent tools such as IMG/M and IMG HMP M. (OpenHelix tutorialThere are other excellent tools that I suggest you check out. QIIME is an excellent tool also.

But the above is not per se a metagenomics tutorial, rather it’s some short screencast of how to use the Galaxy interface for loading data and datatypes. Why? Because another excellent set of tools to use for metagenomic analysis is MetaPhlAn from the Huttenhower lab at Harvard.

The MetaPhlan tools can be downloaded and used ‘offline’, but they also have an excellent Galaxy interface to the tools. If you walk yourself through the MetaPhlAn tutorials on their site, including their Galaxy module one, after familiarizing yourself with Galaxy above, that should help you get started on some excellent metagenomics analysis.

To get a feel of these and other tools and workflows, you might want to browse through this excellent slide set from Surya Saha, Research Associate at Cornell University, from last year.

Quick Links:

Galaxy

Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson & Curtis Huttenhower (2012). Metagenomic microbial community profiling using unique clade-specific marker genes Nature Methods (9), 811-814 : doi:10.1038/nmeth.2066