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The 2020 Workshop on Genomics is being held from 5-18 January, 2020 in Český Krumlov, Czech Republic. This will be the 10th time the Workshop will be held in the Czech Republic.

The Workshop on Genomics was developed in response to the increasing demand for training on how to effectively analyze and manage data generated by modern sequencing technologies. The Workshop curriculum includes extensive coverage of fundamental techniques required of all studies utilizing modern sequence data. The first half of the Workshop focuses on management and modification of modern sequence data files using the Unix command-line and editors to manipulate large data files, best practices for sequence data generation, management and analysis and how to use R to analyze biological data. The second-half of the Workshop is devoted to specific sub-disciplines within the genomic sciences. While these topics may change from year-to-year, efforts are made to devote significant amounts of time to techniques being used widely in the field (e.g. transcriptomics, genome assembly, metagenomics, population genomics).

The Workshop registration fee is $1,800. This amount does not cover travel, lodging or boarding. Many important details about this and other topics can be read on our FAQ page.

A full schedule can be viewed below. Modifications and additions to the schedule may be made at any time prior to the beginning of the Workshop; however, the overall content and structure will remain largely the same.

The Workshop on Genomics is organized by:

Dag Ahren, Lund University

Rayan Chikhi, Institut Pasteur

Sonya Dyhrman, Columbia University

Scott Handley, Washington University

Guy Leonard, University of Exeter

Josephine Paris, University of Exeter

Sophie Shaw, University of Aberdeen

 



Workshop Information

Link to workshop slack

Instance Addresses

T-Shirt Competition

Speed Networking – Monday Night

Faculty Lunches

Bingo Sheets

Group Photo


Week 1 : 5-11 January, 2020

Date Day Time Presenter Topic Location
5 Jan Sunday 6p – 10p Everyone Reception Hotel Zlaty Andel
6 Jan Monday 9a – 12p Scott Handley

Introduction and Orientation

Town Services Presentation

Theater
  Monday 2p – 5p Sonya Dyhrman From flask to field: tracking the drivers of phytoplankton physiological ecology across marine ecosystems Theater
  Monday 7:30p – 10p Everyone Scientific Speed Networking Minorite Monastery
7 Jan Tuesday 9a – 12p Mike Zody Sequencing Technology and Study Design Theater
  Tuesday 2p – 5p Sophie Shaw Introduction to Unix and Software Installation Lab House of Prelate
  Tuesday 7p – 10p Sophie Shaw Working with Sequence Data: Quality Control House of Prelate
8 Jan Wednesday 9a – 12p Mike Zody

Working with Sequence Data: Alignment Introduction| Exercises

House of Prelate
  Wednesday 2p – 5p Mike Zody Variant Calling Lab I – Introduction | Human Variant Calling Exercise | FreeBayes Exercise  House of Prelate
  Wednesday 7p – 10p Mike Zody Variant Calling Lab II House of Prelate
9 Jan Thursday 9a – 12p Antoine Limasset and Camille Marchet Working with Sequence Data: Assembly Theater
  Thursday 2p – 5p Antoine Limasset and Camille Marchet Working with Sequence Data Lab: Assembly House of Prelate
  Thursday 7p – 10p Josephine Paris and Guy Leonard Genomics Lab House of Prelate
10 Jan Friday 9a – 12p Workshop Team Introduction to R and Reproducible Research House of Prelate
  Friday 2p – 5p Malachi Griffith

Genomic Data Visualization and Interpretation 

Genomic Data Visualization Lab I – Introduction to ggplot2

House of Prelate
  Friday 7p – 10p Malachi Griffith

Genomic Data Visualization Lab II – ggplot2 Exercises

House of Prelate
11 Jan Saturday 9a – 12p Evan Eichler Genome Structural Variation Theater
  Saturday 2p – 5p

Rayan ChikhI

and Sergey Nurk

Metagenomics Assembly Lecture, Lab, then Open Lab House of Prelate
  Saturday 6p – 10p Everyone Town Tour and Dinner Town Square


Week 2 : 12-18 January, 2020

Date Day Time Presenter Topic Location
12 Jan Sunday All Day Everyone Free Day You decide!
13 Jan Monday 9a – 12p Brian Haas Transcriptomics Lecture Theater
  Monday 2p – 5p Brian Haas Transcriptomics Lab I House of Prelate
  Monday 7p – 10p Brian Haas Transcriptomics Lab II – Treasure Hunt House of Prelate
14 Jan Tuesday 9a – 12p Kelly Wrighton

Microbial Ecology Lecture 1 (PDF) & Lecture 2 (PDF)

Theater
  Tuesday 2p – 5p Scott Handley Microbiome Lab 1 (lecture) (lab) House of Prelate
  Tuesday 7p – 10p Scott Handley Microbiome Lab 2 House of Prelate
15 Jan Wednesday 9a – 12p Emiliano Trucchi Population Genomics Lecture Theater
  Wednesday 2p – 5p Emiliano Trucchi and Josephine Paris Population Genomics Lab 1 House of Prelate
  Wednesday 7p – 10p Emiliano Trucchi and Josephine Paris Population Genomics Lab 2 House of Prelate
16 Jan Thursday 9a – 12p Christa Schleper Uncovering the Ecological Success and Evolution of Thaumarchaeota Through Ancestral Reconstructions Theater
  Thursday 2p – 5p Kirk Gosik

Single Cell Transcriptomics | GitHub Link

House of Prelate
  Thursday 7p – 10p Kirk Gosik Single Cell Transcriptomics House of Prelate
17 Jan Friday 9a – 12p Chris Wheat Lies, Damn Lies and Genomics Part One | Part Two Theater
  Friday 2p – 5p Everyone

Open Lab – Required Attendance (Certificates and T-Shirts will be issued.)

Transferring Data

House of Prelate
  Friday 7p – 10p Everyone End of Workshop Party You decide!
18 Jan Saturday   Everyone Departure