Querying genome metadata and sequencing projects using Genomes on a Tree (GoaT)

#BGA24/sessions #GoaT #Tools

This session is part of Biodiversity Genomics Academy 2024

Session Leader(s)

Cibele Sotero-Caio
Genomic Data Curator
Tree of Life Programme
Wellcome Sanger Institute

Description

BGA24 will host 2 types of GoaT Web tutorial sessions:

1. GoaT-UI:

Querying metadata on (GoaT) Web

By the end of this session you will:

1. Know what genome-relevant metadata (such as genome size, chromosome number, assembly span) are stored on GoaT
2. Understand the different indexes on GoaT (taxon and assembly) and how to query associated metadata
3. Have experience performing simple and complex queries using GoaT Web Interface to retrieve list of taxa and/or assemblies

• Click to access GoaT-UI presentation slides and session recording

2. GoaT-EBP:

Querying sequencing projects on GoaT Web

By the end of this session you will:

1. Explore Sequencing project pages and reports on GoaT UI
2. Have experience viewing sequencing status and target lists for Earth Biogenome Projects
3. Create and share reports for taxon and assembly metadata

• NOTE: GoaT-EBP session will have 2 instances with same content

• Post-workshop note: The second day covered slightly more material

• Click to access GoaT-EBP_1 presentation slides and session recording

• Click to access GoaT-EBP_2 presentation slides and session recording

Prerequisites

1. Access to web via desktop (GoaT UI is not optimized for mobile)
2. Basic knowledge of genome characteristics and descriptors (assembly, assembly span, genome size, chromosome count, etc.)
3. Interest in Eukaryotic genome sequencing initiatives

!!! warning "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.

More information

GoaT has been built using GenomeHubs to help coordinate efforts across the Earth Biogenome Project (EBP) Network at all stages from planning through sequencing and assembly to publication.

GoaT is described in Challis et al. announcement paper in Wellcome Open Research

• Request tutorials on GoaT GitHub
• Access tutorials on GoaT YouTube Cahnnel