A. Murat Eren (Meren)

Table of Contents

Here you can find a list of past and future anvi’o workshops and events.

We are happy to organize (or participate to) metagenomics workshops given there is interest and we are able. The purpose of this paragraph is to communicate our needs from those who are interested in inviting us to offer a workshop. We are more than happy to consider invitations if our hosts are willing meet the following general requests. These expectations are not written on stone and are open to discussion, however, they help set the stage properly to make sure our mindset is clearly communicated. We generally request institutions to (1) be prepared to host us (usually Meren and Ozcan) for two full days, (2) make the workshop publicly accessible (i.e., keeping 30-40% of the seats to those who may want to attend from outside institutions), (3) offer free lunch to all attendees (since outsiders often struggle to find appropriate places to eat within the time constraints of the dense workshop schedule), and (4) provide coffee and healthy snacks for our breaks. We do not request (or accept even when we are offered) any monetary compensations for our time at workshops we offer, but we except our basic travel expenses to be covered (i.e., economy class flights and basic accommodation at somewhere near the event location). Finally, we request our hosts to consider not charging the participants any attendance fee to maximize the accessibility of these events to underrepresented groups. Thank you very much :)

Temporary notice: While we are happy to organize free microbial ‘omics workshops .. well .. COVID-19 :/

February 2022, Chicago (USA)

Event Metagenomics & Metabolomics Workshop
Dates Feb 18, 2022
Place University of Chicago ((David Rubenstein Forum)[https://davidrubensteinforum.uchicago.edu/])
More info Ruth Fahey

Our first in-person workshop since the start of the COVID-19 pandemic! The Microbiome Center at the University of Chicago hosted this workshop, which included a 2-hour session on metagenomics featuring anvi’o. It was free to attend for people both within and outside the university, and was also broadcast over Zoom. Check out the workshop materials here.

February 2020, Helsinki (Finland)

Event Two-day Intense Anvi’o User Workshop
Dates Feb 25 - 26, 2020
Place University of Helsinki (in this very room)
More info Jenni Hultman, Antti Karkman, or Liisa M Uotila

The Doctoral Programme in Microbiology and Biotechnology at the University of Helsinki is hosting a 2-day anvi’o workshop. They kindly offered 12 seats for those who wish to attend to this free workshop from other institutions. The program also generously promised free lunch and coffee for all participants to make them forget about the cold outside.


October 2019, Brest (France)

Event EBAME Workshop on Computational Microbial Ecogenomics
Dates Oct 19 - Nov 2, 2019
Place European Institute for Marine Sciences at Western Brittany University
More info https://pagesperso.univ-brest.fr/~maignien/ebame5

After years of teaching in many places, I can confidently say that #EBAME is one of the best ‘omics workshops I’ve ever attended. Seriously. The workshop organization, which is led by Lois Maignien, has consistently delivered its top game with infrastructure and socials, and Brest gave us more scenery than we could handle.


October 2018, Brest (France)

Event EBAME Workshop on Computational Microbial Ecogenomics
Dates Sep 29 - Oct 6, 2018
Place European Institute for Marine Sciences at Western Brittany University
More info http://pagesperso.univ-brest.fr/~maignien/ebame4.html

August 2018, Cornwall (United Kingdom)

Event Symposium: Resolving Microbial Communities at Strain-level Resolution
Dates Aug 28 - 31, 2018
Place University of Exeter Cornwall Campus (Penryn, UK)
More info https://metagmicros.weebly.com/


August 2018, Jena (Germany)

Event AquaDiva Genome-Resolved Metagenomics Workshop
Dates Aug 9 - 10, 2018
Place University of Jena
More info Workshop Flyer

Focus: The main focus of this hands-on workshop will be genome-resolved metagenomics, and the opportunities and pitfalls it brings into microbiology. We will cover reconstructing microbial genomes from metagenomes, screening the quality of metagenome-assembled genomes (MAGs), studying their environmental heterogeneity through single-nucleotide variants (SNVs), de-convoluting sub-population genomes using SNV patterns, pangenomics, meta-pangenomics, phylogenomics, and other analyses and visualization strategies to implement comprehensive workflows in order to inverstigate fundamental questions of microbiology.

March 2018, Irvine (USA)

Event Two-day Intense Anvi’o User Workshop
Dates Mar 19 - 20, 2018
Place University of California, Irvine
More info http://merenlab.org/2017/12/25/anvio-workshop-at-uc-irvine/

October 2017, Brest (France)

Event EBAME Workshop on Computational Microbial Ecogenomics
Dates Oct 22 - 27, 2017
Place European Institute for Marine Sciences at Western Brittany University
More info http://pagesperso.univ-brest.fr/~maignien/ebame3.html

Brest 2017

EBAME3 group photo (which even includes Tom Delmont, who was late to the shoot, but Evan Kiefl kindly recovered his running pixels after going through the photo carefully).

Brest 2017

September 2017, Walnut Creek (USA)

Event Two-day Intense Anvi’o User Workshop
Dates Sep 25 - 26, 2017
Place Joint Genome Institute, Walnut Creek, California
More info http://merenlab.org/2017/05/17/anvio-workshop-at-jgi/

JGI 2017

April 2017, Chicago (USA)

Event Two-day Intense Anvi’o User Workshop
Dates Apr 26 - 27, 2017
Place University of Chicago, Chicago, Illinois
More info http://merenlab.org/2017/03/23/anvio-workshop-at-uchicago/

Aftermath: Although how well we did to go through the workshop topics is open to discussion, we probably were most successful at making the most out of the cozy space that was available to us:



Which inspired this haiku from Jessica Mark Welch:

Thirty-eight people
Science, laughter, anvi'o
In a room for twelve
Jessica Mark Welch

Feb 2017, State College (USA)

Event Metagenomics hands-on Workshop
Dates Feb 9, 2017
Place Penn State University, State College, Pennsylvania
More info Please send an e-mail to meren @ uchicago.edu

Dec 2016, Boston (USA)

Event Workshop on Microbial Genome Sequencing
Dates Dec 15, 2016
Place Harvard Medical School, Boston, MA
More info http://cfar.globalhealth.harvard.edu/event/save-date-workshop-microbial-genome-sequencing

Sep 2016, Paris (France)

Event Summer School in Metagenomics
Dates September 12 - 16, 2016
Place Institut Pasteur, Paris, France
More info http://www.france-bioinformatique.fr/
Contact summer_school_metagenomics at groupes dot france-bioinformatique dot fr

There are some very exciting talks during this event. Just so you know.

Sep 2016, Bielefeld (Germany)

Event Joint de.NBI & DZIF training course on targeted and untargeted metagenome analysis
Dates August 29 - September 2, 2016
Place Universitätsstraße 25 (Room V0-133), 33615 Bielefeld, Germany
More info http://www.bioinformatics-platform.dzif.de/?p=1417
Contact Andreas Bremges (andreas.bremges at helmholtz-hzi dot de)

Aug 2016, Montréal (Canada)

The First Traditional Anvi’o Colloquium in Montréal” (hehe) has been quite fun. Myself, Tom Delmont and the 20-some participants of our tiny workshop were pleasantly surprised by the effort Nicolas Tromas put into arranging this event. I thank him and Jesse Shapiro very much for making this a possibility.

We talked a lot about challenges and opportunities emerge from metagenomics, and about using anvi’o as a workbench to explore complex metagenomic data. I thank all participants for their patience, great questions, and feedback!

During the workshop I lost a historical battle, and finally agreed to make the necessary changes for anvi-gen-variability-profile to also report dN/dS for each variable nucleotide position by default. I made very good arguments, but they didn’t work.

I also thank Adrien for this sketch, although it makes me look much cooler than I do:

Our workshop was right after ISME 2016 conference, during which we had many missed interactions with friends and colleagues, which made it totally worth carrying an anvi’o poster all they way to Montreal:

For people who are interested in a higher resolution, a PNG file for the poster is also here: eren-isme-poster-72dpi.png.

Event The First Traditional Anvi’o Colloquium in Montréal
Dates August 29 - 30, 2016
Place Uniersity of Montréal, Montréal, Canada
More info http://merenlab.org/2016/03/13/worskhop-at-montreal/
Contact Nicolas Tromas (tromas.nicolas at gmail dot com)

Aug 2016, Woods Hole (USA)

STAMPS was very exciting this year. This was the first time Tom and I presented anvi’o to a large crowd, and heard back some very encouraging feedbacks:

I guess we will continue working on anvi’o after these!

Here is a group photo (which is pretty much my job during every STAMPS course since 2011):


Event STAMPS Course
Dates 3 - 13 August, 2016
Place Marine Biological Laboratory, Woods Hole, USA
More info https://stamps.mbl.edu/
Contact David Mark Welch (dmarkwelch at mbl dot edu)

July 2016, Hawai’i (USA)

ECOGEO covered multiple topics. The first day there was a UNIX tutorial by Ken, and lots of marker gene stuff from multiple people. The second day there were four modules: assembly, binning, annotation, and phylogenetics. I -for the first time- used anvi’o to compare binning tools.

Here is Ken teaching UNIX to the class the first day:


Event ECOGEO Workshop
Dates 25 - 26 July, 2016
Place Marine Biological Laboratory, Woods Hole, USA
More info http://earthcube.org/group/oceanography-geobiology-environmental-omics
Contact ECOGEO (ecogeo.rcn at gmail dot com)