Pangenome Assembly and Assessment using Minigraph and Bandage

This session is part of Biodiversity Genomics Academy 2023

Session Leader(s)

Zachary Cohen, Insect Cotton Control and Disease Research Unit. USDA-ARS, College Station, TX, USA

Description

Welcome to this data-to-figure workshop on pangenome assembly using minigraph and bandage! In this session you will first get a brief background on the utility of pangenomes, followed by a hands-on tutorial where you will:

1. construct a pangenome using minigraph and primate mitochondrial genomes
2. visualize and annotate using bandage
3. identify lineage specific differences

By the end of this session, you will have all of the tools necessary to curate your genome assemblies into a functional and dynamic reference graph.

Prerequisites

To get the most out of this workshop, participants will have downloaded the requisite programs: minigraph, bandage, as well as the data fasta file of mitochondrial gene transcripts. Experience with GUI point-n-click programs, access and familiarity with terminal and bash command line programming grep, cd, ls ...etc.

Please make sure you MEET THE PREREQUISITES and READ THE DESCRIPTION above

You will get the most out of this session if you meet the prerequisites above.

Please also read the description carefully to see if this session is relevant to you.

If you don't meet the prerequisites or change your mind based on the description or are no longer available at the session time, please email tol-training at sanger.ac.uk to cancel your slot so that someone else on the waitlist might attend.