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Accessing Livestock Resources in Ensembl

Genome assembly is cheaper, more accurate and more automated than it has ever been. This is due to a combination of more cost-efficient chemistries, new sequencing technologies and better algorithms. The livestock community has been at the forefront of this new wave of genome assembly, generating so...

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Autores principales: Martin, Fergal J., Gall, Astrid, Szpak, Michal, Flicek, Paul
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8115729/
https://www.ncbi.nlm.nih.gov/pubmed/33995484
http://dx.doi.org/10.3389/fgene.2021.650228
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author Martin, Fergal J.
Gall, Astrid
Szpak, Michal
Flicek, Paul
author_facet Martin, Fergal J.
Gall, Astrid
Szpak, Michal
Flicek, Paul
author_sort Martin, Fergal J.
collection PubMed
description Genome assembly is cheaper, more accurate and more automated than it has ever been. This is due to a combination of more cost-efficient chemistries, new sequencing technologies and better algorithms. The livestock community has been at the forefront of this new wave of genome assembly, generating some of the highest quality vertebrate genome sequences. Ensembl’s goal is to add functional and comparative annotation to these genomes, through our gene annotation, genomic alignments, gene trees, regulatory, and variation data. We run computationally complex analyses in a high throughput and consistent manner to help accelerate downstream science. Our livestock resources are continuously growing in both breadth and depth. We annotate reference genome assemblies for newly sequenced species and regularly update annotation for existing genomes. We are the only major resource to support the annotation of breeds and other non-reference assemblies. We currently provide resources for 13 pig breeds, maternal and paternal haplotypes for hybrid cattle and various other non-reference or wild type assemblies for livestock species. Here, we describe the livestock data present in Ensembl and provide protocols for how to view data in our genome browser, download via it our FTP site, manipulate it via our tools and interact with it programmatically via our REST API.
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spelling pubmed-81157292021-05-13 Accessing Livestock Resources in Ensembl Martin, Fergal J. Gall, Astrid Szpak, Michal Flicek, Paul Front Genet Genetics Genome assembly is cheaper, more accurate and more automated than it has ever been. This is due to a combination of more cost-efficient chemistries, new sequencing technologies and better algorithms. The livestock community has been at the forefront of this new wave of genome assembly, generating some of the highest quality vertebrate genome sequences. Ensembl’s goal is to add functional and comparative annotation to these genomes, through our gene annotation, genomic alignments, gene trees, regulatory, and variation data. We run computationally complex analyses in a high throughput and consistent manner to help accelerate downstream science. Our livestock resources are continuously growing in both breadth and depth. We annotate reference genome assemblies for newly sequenced species and regularly update annotation for existing genomes. We are the only major resource to support the annotation of breeds and other non-reference assemblies. We currently provide resources for 13 pig breeds, maternal and paternal haplotypes for hybrid cattle and various other non-reference or wild type assemblies for livestock species. Here, we describe the livestock data present in Ensembl and provide protocols for how to view data in our genome browser, download via it our FTP site, manipulate it via our tools and interact with it programmatically via our REST API. Frontiers Media S.A. 2021-04-28 /pmc/articles/PMC8115729/ /pubmed/33995484 http://dx.doi.org/10.3389/fgene.2021.650228 Text en Copyright © 2021 Martin, Gall, Szpak and Flicek. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Martin, Fergal J.
Gall, Astrid
Szpak, Michal
Flicek, Paul
Accessing Livestock Resources in Ensembl
title Accessing Livestock Resources in Ensembl
title_full Accessing Livestock Resources in Ensembl
title_fullStr Accessing Livestock Resources in Ensembl
title_full_unstemmed Accessing Livestock Resources in Ensembl
title_short Accessing Livestock Resources in Ensembl
title_sort accessing livestock resources in ensembl
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8115729/
https://www.ncbi.nlm.nih.gov/pubmed/33995484
http://dx.doi.org/10.3389/fgene.2021.650228
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