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5th EBAME Workshop on Computational

Microbial Ecogenomics

October 19 - November 2 , 2019 in Brest - France
(application deadline May 13 , 2019)

Microbial Ecology is undergoing rapid evolution and dramatic progresses thanks to the combined advances in next-generation DNA sequencing technologies and computational approaches for data analysis and visualization. As a result,‘microbial ecogenomics’ has become an essential part of investigations of marine or terrestrial habitats, or host-microbe interactions. The aim of the EBAME workshop is to bring together researchers who generate complex ‘omics datasets to investigate biologically significant questions with researchers who develop new ways to analyze complex datasets.

The workshop will have lectures on new methods
and their applications on real-world datasets, and  tutorials for hands-on experience.

The workshop will focus on various state-of-the-art data analysis practices targeting genome-resolved metagenomics including recovery of population genomes from metagenomes, analysis of micro-diversity through single-nucleotide variants, strain deconvolution, comparative genomics, application of network theory to complex metagenomic data, and data visualization.
Check EBAME 2018 program and faculty


The workshop will be held exclusively in English and hosted by the European Institute for Marine Sciences at Western Brittany University, from  October 19 to  November 2, 2019. The institute is located on the wonderful setting of the Bay of Brest, at the heart of the largest French marine science campus, with easy access from Brest Bretagne international airport and train station.

Attendance Fee
Fee of 650€ per attendee for the 2 weeks workshop participation. It includes lunch meals, snacks, coffee breaks
and housing in small houses on the waterfront.

The workshop organization is made possible thanks to the financial support of the ISBLUE graduate school, the IUEM Marine Science Institute, the region Bretagne and the Brest University research council  the  Brest Metropole BMO and the FACE / Thomas Jefforson fund.

Who should apply
The workshop will be most useful for researchers and graduate students who study microbes via shotgun genomics, metagenomic or metatranscriptomic datasets, and are interested in genome-resolved metagenomics and pangenome analysis. Applicants from different backgrounds are most welcome (such as computer scientists or biostatisticians). Hands-on tutorials will require familiarity with the UNIX terminal environment.

How to apply
An e-mail titled ‘EBAME 2019 Application’ with application material as PDF attachments should be sent to lois.maignien@univ-brest.fr. Please make sure your application includes a short statement with your scientific background, current interests, the kinds of datasets you are currently working with, and expectations from the workshop (ideally in a single page). Feel free to add your CV as a separate PDF file to your application. We will consider applications until May 13, 2019.
Applicants will be notified shortly after regarding participation.

Thank you for your interest and we are looking forward to meeting you in Brest!

On behalf of the workshop faculty,

The organizing committee

EBAME4 alumni words....

"A top experience in theoretical and practical microbial ecogenomics, in a beautiful and inspiring spot of Brittany. Ideal for deepening your scientific knowledge while widening your network of contacts around Europe and the world"

"As a marine ecologist, specialized in ecosystem modelling but collaborating with colleagues on marine metagenomics for a few years now, I was eager to dig into metagenomics data by myself and learn how to handle, analyse and interpret such huge datasets. The EBAME workshop entirely fulfilled my needs and expectations. I have learned a lot from world-class experts on the topic. Even if the week was quite intense, loaded with many lectures and training sessions, I have also spend a wonderful time with peers, in a very friendly atmosphere. The organising staff was very helpfull and nice. Thank very much for this great experience. I will advertise it around me."

"EBAME was a very informative and hands-on workshop that made me aware of some of the newest tools for metagenome analysis that can be applied in a variety of research fields. In the lectures, we could learn both about the theoretical principles behind these tools as well as about real studies that implemented them. I would strongly recommend the workshop to anyone with some background in bioinformatics and that is interested in microbial ecology and willing to contact and collaborate with people from related research areas."

"I'm research engineer in bioinformatics and the EBAME workshop was very helpful for me. It is the first workshop in France (to my knowledge) that gives us both theorical and practical course to analyze complex and large metagenomic datasets. Metagenomic tools and sequencing technologies evolve very rapidly and this workshop was a good opportunity to have a global view on metagenomics, discover tools and practices, as well as get advices and caveat for metagenomic analysis. This workshop will be very helpful for my current work, and I was also very happy to discuss metagenomics with people working on very diverse ecosystems. Thank you! "

"I loved this workshop! It was really interesting and useful to get an overview of the possibilities of metagenomics data. The latest techniques were covered by experts in the field. These people, who spend a lot of their time on figuring out the best approaches, shared their insights and pointed us in the right direction for methods, tools etc. Before metagenomics analyses would've been such a huge effort, I wouldn't have started on it, but now it has really become accessible to me"

"The organization was great, organizers were really helpful, lectures and practical sessions were greatly useful and new knowledge/skills were learned"

"Very glad I came. It was more specifically useful that I expected. I have been to many workshops, but I have to admit this is one of the best so far. Highly qualified teachers and very helpful computer assistant makes this workshop very effective. I just started working on metagenome data and I didn't know where to start? I never did manual binning and construct genome from metagenome data. Certainly, after attending this workshop, I can add these two very difficult yet important skills to my resume, which is very significant for any researcher who works on metagenome data."

"Being able to spend a week with tool makers and first-class metagenomics scientists is invaluable. I'll come back next year."

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