Microbial 'omics

Table of Contents

This document was last updated on June 7th, 2016.

We are thankful to Illumina, FAS, Eppendorf, FRQNT and GRIL for their support.


Nicolas Tromas, who is currenlty a post-doctoral researcher in B. Jesse Shapiro’s group at the University of Montréal came up with this great idea: A 2-days anvi’o workshop at the university, right after ISME 2016.

ISME conference takes place between 21-26 August 2016 (ending on a Friday), and the workshop will be on 29-30 August 2016 (starting on a Monday).

The date and place is the only certainty at this point, but we wanted to start publicizing it in case you are planning to go for ISME, actively working on shotgun metagenomic data, the idea of extending your stay to spend a weekend in Montréal, and then attending to a free workshop sounds appealing to you. We keep updating this post as the schedule starts to take shape.

We are planning to limit the number of attendees to 15. Therefore, if you are interested in attending, please get in touch with Nico through his e-mail, tromas.nicolas [AT] gmail [DOT] com.

Topics and Schedule

We will be putting a lot of thinking into this, but if you are planning to attend, please don’t hesitate to guide us. Here is a couple of bullet points we currently have in mind:

  • The focus of the workshop will be on the recovery and curation of environmental genomes through assembly-based binning practices using anvi’o in conjunction with CONCOCT, or MetaBAT.

  • Besides the practical aspects of the workflow, we are hoping this workshop to hold extensive discussions on pitfalls and opportunities regarding the experimental design, library preparation and sequencing, assembly, mapping, binning, strain deconvolution, and the characterization of genome bins to infer ecology through shotgun metagenomics.

  • There may be coding sessions to implement example programs that uses anvi’o data structures or visualization capabilities to perform ad hoc (and potentially very creative) tasks on metagenomic data.

  • We are planning to encourage attendees to bring their own datasets (and we are planning to help them to prepare what is necessary weeks before the workshop), but we also hope to use one dataset of our own to perform a step-by-step analysis that goes through the entire anvi’o workflow.

Too ambitious to fit into two days? Well. We will see that!

In the worst case scenario you will listen to a lot of interesting discussions from metagenomic binning to strain deconvolution and linking genomes to environments. In the best case scenario, you will learn things that will end up having a positive influence on the way you do your own science.

Logistics

Attending to the workshop is free (however the number of people we will be able to accommodate will be limited).

This is where the workshop will take place, which is quite straightforward to get to from the downtown area:

Université de Montréal
Département des Sciences Biologiques
Pavillon Marie-Victorin
90, avenue Vincent-d’Indy
Local A-220 (2nd floor, street level)
Montréal (Québec)
--- Once you are in Montréal, you can take the **Blue Line metro station Édouard-Montpetit**, or take **Bus 51** or **Bus 129**. It seems Uber also works. ## Attendees Here is an incomplete list of people who are likely going to be at the workshop (we will keep this list up-to-date as things get clearer): |Name|Affiliation|Info| |:--|:--|:--:| |B. Jesse Shapiro|University of Montréal|[Web](http://www.shapirolab.ca/peoplepersonel.html), [Twitter](https://twitter.com/bjesseshapiro)| |A. Murat Eren|University of Chicago|[Web](http://merenlab.org), [Twitter](http://twitter.com/merenbey), [Github](http://github.com/meren)| |Nicolas Tromas|University of Montréal|[Web](https://www.researchgate.net/profile/Nicolas_Tromas)| |Tom O. Delmont|University of Chicago|[Twitter](http://twitter.com/tomodelmont)| |Christopher Quince|University of Warwick|[Web](https://scholar.google.com/citations?user=0yKnJ2wAAAAJ&hl=en)| If you have any questions or suggestions, please don't hesitate to get in touch with me (meren [AT] uchicago [DOT] edu) or Nico (tromas.nicolas [AT] gmail [DOT] com).