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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...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
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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 |
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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 |