Tag Archives: metagenomics


Video Tip of the Week: JGI user meeting videos, and MetaSUB

Mason JGIThis week’s Video Tip of the Week is actually a whole bunch of videos. Although I’ll highlight one here as our tip, there are many great talks from the recent JGI Genomics of Energy & Environment meeting. Although typically we focus on specific software tools for our tips, I think this is a nice case of also looking at the type of research done with the tools.

This is a nice example of how to make a meeting accessible for a lot of people as well, using multiple strategies. The video channel, a Storify, dropboxes of slides (below), and the agenda details can help you to decide what might be relevant for your work. For example, we’ve talked about Docker, but you can now see how it’s deployed by the folks who are talking about it here. There’s a talk with Phytozome. And much more.

For today I’ll highlight MetaSub as one of the projects from the Mason lab. The Mason lab has participated in projects you probably heard about in the media–including swabbing the NYC subway system. You can see that data at PathoMap. MetaSUB stands for a data collection effort coming up soon, the Metagenomics & Metadesign of Subways and Urban Biomes. A global swabbing festival of the 10 busiest subways in the world (including my own–I wonder if I can do the station in my neighborhood?), to get more geospatial metagenomics maps, find antimicrobial resistance markers, and look for new biosynthetic gene clusters. It will be held on June 21, 2016–the summer solstice. It will tell us way more about our urban environments than we currently know. Maybe too much. But it’s a great idea, sure to reveal things we don’t know about our lived environment right now.

And here are the slides for the talk, as promised in the video. Mason tweets them:

He seriously did get through those 138 slides in 30 minutes. I was skeptical when I downloaded them before watching through them with the talk–but he really managed it. I was kind of out-of-breath just watching it.

He also talked about extreme environment sampling, and MetaPhlan2 and HUMAnN2 analyses, in a later segment. The whole thing is an excellent and breezy discussion of real-world genomics and a lot of appealing stories that the public would connect with. They are also doing educational outreach with a HTGAA course (How To Grow Almost Anything). There some really fun stuff with the Gowanus canal (seriously), and so much opportunity just hanging around in our cities. But also–what’s growing in space. They are working on space station mold. And astronauts–the NASA twins. They are also sending up a MinION (which they checked to see would work in microgravity–see paper below).

It was a very engaging talk. From an apparently very busy guy.

Hat tip:

Quick links:

PathoMap: http://www.pathomap.org/

MetaSUB:  http://www.metasub.org/


Afshinnekoo, E., Meydan, C., Chowdhury, S., Jaroudi, D., Boyer, C., Bernstein, N., Maritz, J., Reeves, D., Gandara, J., Chhangawala, S., Ahsanuddin, S., Simmons, A., Nessel, T., Sundaresh, B., Pereira, E., Jorgensen, E., Kolokotronis, S., Kirchberger, N., Garcia, I., Gandara, D., Dhanraj, S., Nawrin, T., Saletore, Y., Alexander, N., Vijay, P., Hénaff, E., Zumbo, P., Walsh, M., O’Mullan, G., Tighe, S., Dudley, J., Dunaif, A., Ennis, S., O’Halloran, E., Magalhaes, T., Boone, B., Jones, A., Muth, T., Paolantonio, K., Alter, E., Schadt, E., Garbarino, J., Prill, R., Carlton, J., Levy, S., & Mason, C. (2015). Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics Cell Systems, 1 (1), 72-87 DOI: 10.1016/j.cels.2015.01.001

Alexa B.R. McIntyre, Lindsay Rizzardi, Angela M Yu, Gail L. Rosen, Noah Alexander, Douglas J. Botkin, Kristen K. John, Sarah L. Castro-Wallace, Aaron S. Burton, Andrew Feinberg, & Christopher E. Mason (2015). Nanopore Sequencing in Microgravity bioRxiv DOI: 10.1101/032342

Friday SNPpets

This week’s SNPpets include a range of tools and genomics studies, from microbial to planaria to salmon to humans, as usual–as well as some that are species-agnostic.  Also stuff that is aimed at drug targets and pharmacology, including the Open Targets project Target Validation Platform. There’s a new DNA privacy bill under discussion in the US that I found interesting. Also–next Monday April 25 is #DNADay! Participate in community outreach with a number of strategies.

SNPpets_2Welcome 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

This week’s SNPpets offer both science and humor. I think people get a little punchy around the holidays/end of semester. There’s software for assembly, a bioinformatics network for African topics, bioethics of gene editing, cancer and personalized medicine,  Dilbert comments on big data and health, interesting tools for open- and evidence-based medicine, microbiome concepts and a metagenomic journey. Most curious thing this week: the mouse poem constructed entirely from paper titles.

SNPpets_2Welcome 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…

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:


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.