From listmaster animalgenome.org Tue Sep 16 09:44:03 2025
From: Francesca Bernini <francesca.berniniunimi.it>
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: Brenda Murdoch - Tomorrow's #animalgenomics nf-core Special
Interest Group Meeting at 4 PM CEST
Date: Tue, 16 Sep 2025 09:44:04 -0500
Dear all,
We are pleased to announce that Brenda Murdoch (professor at the Department
of Animal, Veterinary and Food Sciences at the University of Idaho) will be
the speaker tomorrow at the #animal-genomics Special Interest Group meeting,
taking place at 16:00 CEST.
Find below the abstract of her talk:
Pangenomes, represented as variation graphs, have become valuable genomic
resources for investigating the breadth of genetic diversity across species.
These graphs capture various types of genetic variation including single
nucleotide variants (SNVs), structural variants (SVs), and copy number
variants (CNVs) which contribute significantly to phenotypic diversity
within and between species. The Ovis genus exhibits extensive biodiversity
and phenotypic variation. In this study, we utilize a pangenome constructed
from 25 sheep breeds—comprising 22 domestic breeds and three wild
relatives—to investigate the genetic drivers of trait variation within Ovis.
We compare two tools for constructing variation graphs: Pangenome Graph
Builder (PGGB) and Minigraph- Cactus (MC). PGGB captures a broader spectrum
of genetic variation, resulting in more complex graphs, whereas MC
simplifies graph structure through pruning, making it more suitable for
downstream genotyping. We discuss the computational challenges associated
with processing PGGB graphs, particularly the increased resource demands.
Additionally, we present examples of SVs identified through these graphs
that are linked to known biological traits in sheep. While variation
graph-based approaches offer powerful insights into SVs within species,
the computational burden of genotyping short reads using complex graphs
remains a significant limitation.
More information on https://nf-co.re/...g_animalgenomics_sep
Join Zoom Meeting https://rediris.zoom.us/j/99370728121
Meeting ID: 993 7072 8121
Looking forward to seeing you,
Francesca Bernini
The nf-core #animal-genomics group is an open group for anyone interested
in using/developing nf-core tools tailored for animal genomics. It provides
a collaborative space to share expertise, troubleshoot, and stay updated
with the latest developments. For more information about it please watch
this nf-core bytesize talk introducing the group:
https://youtu.be/2vqHkveWAws or visit our site:
https://nf-co.re/...oups/animal-genomics
Our primary communication platform is Slack. We warmly invite you to become
part of the conversation and its vibrant community by joining the nf-core
Slack (https://nf-co.re/join/slack) and the #animal-genomics channel.
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