Pangenomics Workshop

Application: Fill out this online application here: Pangenomics Workshop Application

Space is limited!

When

February 12-16, 2024

Where

Virtual (by the National Center for Genome Resources (NCGR) Santa Fe, NM)

Audience

This program is geared towards training biologists (undergraduates, graduates and researchers) with minimal or no bioinformatics experience. Space is limited.

Topic Overview

The proliferation of reference quality genome assemblies within any single species has necessitated the need for pangenome analyses. Such analyses remove reference-bias and elucidate biological signals at a more comprehensive population scale. In this workshop, students will learn what exactly a pangenome is, how to build a pangenome, and how to perform fundamental bioinformatic analyses on pangenomic data.

Objective

Students will learn to use the command-line interface to conduct graphical pangenome analyses. Specifically, students will learn to build pangenome graphs using vg, minigraph, and Cactus. They will learn to visualize these pangenomes using Bandage and IGV, and they will learn how to map reads and call variants on the graphs, comparing both run-time and mapping performance between methods. Additionally, students will be given an overview of other, interoperable tools to broaden their understanding of the rapidly moving pangenomics space.

Prerequisites

Unix, sequencing basics and other study guides will be provided upon acceptance.

What to expect upon acceptance

Email confirming acceptance into the internship program and further details.

Logistics

The workshop will be conducted virtually using primarily Zoom as our conferencing platform. We will also use a variety of other software and tools, and you will log onto NCGR’s Unix analysis server for the command line tools. After the workshop, students can use our analysis server for their research or education purposes for up to one year.

Late applications will not be accepted. Selection Committee to select participants shortly after the deadline. If any questions arise while reviewing your application packet, we will contact you directly.

Contact

Please contact Project Coordinator, Ethan Price, with any additional questions you may have at and we look forward to your participation!

Sponsored by New Mexico IDeA Network for Biomedical Research Excellence (NM-INBRE).