Hands-on SARS-CoV-2 genome analysis workshop

Please also take a look at the companion symposium celebrating the 1 year anniversary of COV-IRT on March 31.


Registration for this event has closed.

The Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC), Rice University, the COVID-19 International Research Team (COV-IRT), DNAnexus, and the BCM Alkek Center for Metagenomics and Microbiome Research (CMMR) are organizing a two day workshop (March 29-30, 8 a.m.-5 p.m. CDT) detailing the analysis of SARS-Cov-2 sequencing data, from raw read data to variant analyses and phylogenetic inference. The workshop aims at establishing best analysis practices for the community and training scientists in handling virus RNA data from raw fastq files to phylogenetic analysis and comparison. The workshop is split in four modules:

  • Sequencing and QC
  • Read mapping and variant calling
  • Reference-guided assembly and low frequency variant calling
  • Phylogenetic and transmission analysis

Each module will be split between a short theory lecture and a longer hands-on lecture to familiarize participants with the methods/tools at hand and with the discussed analysis steps. The data sets and methods will be provided over compute instances from DNAnexus.

We welcome registration from everyone, but will limit the workshop at 50 participants. Workshop participants will be selected based on registration responses.

What can you expect?

At the end of the workshop participants will have a profound knowledge of the state of the art computational methods as well as how to apply them and chain them together to undertake a full analysis. In addition, we will discuss the parameters and the pros and cons of certain methods and approaches.

The lectures and instruction manual will be made available during the course of this workshop to promote open science and open sharing of knowledge.

Who is the target audience?

We are looking for participants that are not well versed in the analysis of SARS-CoV-2 to further foster independent research across the USA or around the world.

This workshop will take place on a command line interface. We will provide an introduction, but if you never used a LINUX system before this might require additional training before the workshop.

What do you require to attend?

Given the current citation of SARS-Cov-2 this workshop will be held remotely. As such each participant needs a working laptop with a stable internet connection. The lectures and hands-on instructions will be given remotely using Remo. Each participant will operate on their own command line via an interface of DNAnexus. The first part of the workshop will introduce and provide guidance on how the basics of getting up and running.

The Instructor Team

Module 1: Sequencing and QC

Lead: Sara J Javornik Cregeen
Baylor College of Medicine

Module 2: Read mapping and variant calling

Lead: Fritz J Sedlazeck
Baylor College of Medicine

Module 3: Reference-guided assembly and low frequency variant calling

Lead: Todd Treangen
Rice University

Module 4: Phylogenetic and transmission analysis

Lead: Nídia Trovão
Fogarty International Center, NIH

Registration for this event has closed.