Cargando…

Genomer — A Swiss Army Knife for Genome Scaffolding

The increasing accessibility and reduced costs of sequencing has made genome analysis accessible to more and more researchers. Yet there remains a steep learning curve in the subsequent computational steps required to process raw reads into a database-deposited genome sequence. Here we describe “Gen...

Descripción completa

Detalles Bibliográficos
Autores principales: Barton, Michael D., Barton, Hazel A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691230/
https://www.ncbi.nlm.nih.gov/pubmed/23826173
http://dx.doi.org/10.1371/journal.pone.0066922
_version_ 1782274442845487104
author Barton, Michael D.
Barton, Hazel A.
author_facet Barton, Michael D.
Barton, Hazel A.
author_sort Barton, Michael D.
collection PubMed
description The increasing accessibility and reduced costs of sequencing has made genome analysis accessible to more and more researchers. Yet there remains a steep learning curve in the subsequent computational steps required to process raw reads into a database-deposited genome sequence. Here we describe “Genomer,” a tool to simplify the manual tasks of finishing and uploading a genome sequence to a database. Genomer can format a genome scaffold into the common files required for submission to GenBank. This software also simplifies updating a genome scaffold by allowing a human-readable YAML format file to be edited instead of large sequence files. Genomer is written as a command line tool and is an effort to make the manual process of genome scaffolding more robust and reproducible. Extensive documentation and video tutorials are available at http://next.gs.
format Online
Article
Text
id pubmed-3691230
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-36912302013-07-03 Genomer — A Swiss Army Knife for Genome Scaffolding Barton, Michael D. Barton, Hazel A. PLoS One Research Article The increasing accessibility and reduced costs of sequencing has made genome analysis accessible to more and more researchers. Yet there remains a steep learning curve in the subsequent computational steps required to process raw reads into a database-deposited genome sequence. Here we describe “Genomer,” a tool to simplify the manual tasks of finishing and uploading a genome sequence to a database. Genomer can format a genome scaffold into the common files required for submission to GenBank. This software also simplifies updating a genome scaffold by allowing a human-readable YAML format file to be edited instead of large sequence files. Genomer is written as a command line tool and is an effort to make the manual process of genome scaffolding more robust and reproducible. Extensive documentation and video tutorials are available at http://next.gs. Public Library of Science 2013-06-24 /pmc/articles/PMC3691230/ /pubmed/23826173 http://dx.doi.org/10.1371/journal.pone.0066922 Text en © 2013 Barton, Barton http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Barton, Michael D.
Barton, Hazel A.
Genomer — A Swiss Army Knife for Genome Scaffolding
title Genomer — A Swiss Army Knife for Genome Scaffolding
title_full Genomer — A Swiss Army Knife for Genome Scaffolding
title_fullStr Genomer — A Swiss Army Knife for Genome Scaffolding
title_full_unstemmed Genomer — A Swiss Army Knife for Genome Scaffolding
title_short Genomer — A Swiss Army Knife for Genome Scaffolding
title_sort genomer — a swiss army knife for genome scaffolding
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691230/
https://www.ncbi.nlm.nih.gov/pubmed/23826173
http://dx.doi.org/10.1371/journal.pone.0066922
work_keys_str_mv AT bartonmichaeld genomeraswissarmyknifeforgenomescaffolding
AT bartonhazela genomeraswissarmyknifeforgenomescaffolding