Tag Archives: metagenomics

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

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

  • This is not a bad idea. Boston Sci-Geek Tours. I used to work for the Park Service. Hmmm… RT @YishaiKnobel: Fascinating tour and lecture on genomics at Broad Institute today.  Broad should be turned into a Boston tourist attraction. [Mary]
  • RT @BioCatalogue: The BioCatalogue iPhone/iPad app by @manniet3 is now out! http://bit.ly/p2tUQF Please do let us know what you think. [Mary]
  • Includes KEGG, iPATH 2.o, PathwayProjector, metaSHARK, MEGAN 4,  HUMAnN: RT @phylogenomics: A Survey of Metabolic Reconstruction Tools for Metagenomic Datasets » The Bioinformatics Knowledgeblog http://shar.es/HK0U5 [Mary]
  • A Special Symposium Celebrating the 40th Anniversary of the Protein Data Bank, October 28 – 30, 2011, Cold Spring Harbor, NY – Poster Abstract deadline: August 15 [Jennifer]
  • Oh yes, plz: RT @nutrigenomics: like RT @grapealope: Bioinformatics is not just about building tools. We know our tools; we should use them first. @atulbutte #singularityu [Mary]
  • Giggle. I’ve done this with several species, not just plants… : @pcronald: Botanist holds up the entire salad bar. http://onion.com/pojv2t [Mary]
  • RT @wahwahnyc: On PubMed Central: The PathOlogist: an automated tool for pathway-centric analysis. BMC Bioinformatics. http://1.usa.gov/oDyBpc [Mary]
  • Looking for some geeky fun? The Twenty-First 1st Annual Ig Nobel Prize ceremony will occur Thursday, September 29, 2011 and tickets are on sale now. Note: “The Ig Nobel Prizes honor achievements that first make people laugh, and then make them think.” [Jennifer]
  • RT @genetics_blog: . @PLoS and @mendeley_com Call for Apps: http://bit.ly/oc2NGL and http://bit.ly/nHYqNa [Mary]
  • Just saw this in Nature News about Google and Microsoft: Computing giants launch free science metrics [Jennifer]
  • FameLab, a science and engineering communication competition – I haven’t seen an uninteresting one yet… [Jennifer]

What’s the answer? Open thread

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

BioStar Question of the Week:

List of completed genome projects and metagenomics projects : I am looking for a website / slide / figure that provide the list or statistics of completed genome projects and metagenomics projects (as of 2010). As indicated in an earlier discussion at BioStar, GOLD provides some statistics, but only up to 2009 and no information is indexed about metagenomics projects.

– by Khader Shameer

The highly-rated and selected top answer provided a couple of links that delivered some useful links for eukaryotes, prokaryotes, and metagenomics as well. But it was also edited to provide the list of the species counts over the years, which was a very interesting year to year view of the growth (in most cases). Check out the answers for the details.

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Metagenomic Resources from The National Academy of Science

Father’s Day I’m not sure how parents & metagenomics have gotten connected for me, but it seems they have.  You may remember my Mother’s Day post.  This past weekend my in-laws were visiting us for Father’s Day and a lot of the discussion involved recounting news stories about the tomato-associated salmonella outbreaks & quizzing the family biologist (me) on the subject.  Monday morning I wished our house guests a safe journey home & then checked my OpenHelix email account – to find an email from Mary telling me she had just gotten a metagenomics poster in her new issue of Nature Biotechnology.  (We always try to ‘share the wealth’ with each other, and you guys too, actually.)  The poster came with a web address, which I of course checked out.  Turns out …

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Metagenomics making the big Times (as in NY)

Metagenomics, which is really a new area of study (barely this last decade) in comparison to most biological areas of research, is already making into the mainstream press. The New York Times has an article yesterday entitled “Bacteria thrive in the inner Elbow, No Harm Done” (you’ll need a free registration to read that). The article quotes from metagenomic studies that show that our inner elbows contain a unique microbiome of species even in comparison to our upper arm, though it goes a  more into metagenomic studies than just that. As the article states:

The research is part of the human microbiome project, microbiome meaning the entourage of all microbes that live in people.
The project is an ambitious government-financed endeavor to catalog the typical bacterial colonies that inhabit each niche in the human ecosystem.

That’d be this project. The article does a decent job of explaining why this project is helpful, but doesn’t really explain how this approach of metagenomics is different or how it’s done (in fact, it never says the word “metagenomics“). Oh well, can’t have everything.

For your edification: There is last year’s report “The New Science of Metagenomics” from the National Research Council (you can read free online, or purchase as a book. Also, of course there are at least two extensive databases of metagenomic data, IMG/M (free tutorial) and Camera.

Metagenomics

Just a short post with some information:

Metagenomics is the new genomics :). NIH Roadmap has a new initiative, the Human Microbiome Project with a bit of funding :) . Meanwhile, other projects and databases are developing such as Integrated Microbial Genomes w/ Microbiome Samples (or IMG/M) and Camera. It’s an exciting and fascinating field (my former colleagues at the Bork lab just published interesting research in this field), though some scientists of course have their doubts.