ORPER: A Workflow for Constrained SSU rRNA Phylogenies

The continuous increase in sequenced genomes in public repositories makes the choice of interesting bacterial strains for future sequencing projects ever more complicated, as it is difficult to estimate the redundancy between these strains and the already available genomes. Therefore, we developed t...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Luc Cornet, Anne-Catherine Ahn, Annick Wilmotte, Denis Baurain
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	cyanobacteria SSU (16S) rRNA phylogenomics sequencing workflow ribosomal proteins Genetics QH426-470
Acceso en línea:	https://doaj.org/article/916e9e17720f4201a57bd721580ee287
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:916e9e17720f4201a57bd721580ee287
record_format	dspace
spelling	oai:doaj.org-article:916e9e17720f4201a57bd721580ee2872021-11-25T17:41:26ZORPER: A Workflow for Constrained SSU rRNA Phylogenies10.3390/genes121117412073-4425https://doaj.org/article/916e9e17720f4201a57bd721580ee2872021-10-01T00:00:00Zhttps://www.mdpi.com/2073-4425/12/11/1741https://doaj.org/toc/2073-4425The continuous increase in sequenced genomes in public repositories makes the choice of interesting bacterial strains for future sequencing projects ever more complicated, as it is difficult to estimate the redundancy between these strains and the already available genomes. Therefore, we developed the Nextflow workflow “ORPER”, for “ORganism PlacER”, containerized in Singularity, which allows the determination the phylogenetic position of a collection of organisms in the genomic landscape. ORPER constrains the phylogenetic placement of SSU (16S) rRNA sequences in a multilocus reference tree based on ribosomal protein genes extracted from public genomes. We demonstrate the utility of ORPER on the Cyanobacteria phylum, by placing 152 strains of the BCCM/ULC collection.Luc CornetAnne-Catherine AhnAnnick WilmotteDenis BaurainMDPI AGarticlecyanobacteriaSSU (16S) rRNAphylogenomicssequencingworkflowribosomal proteinsGeneticsQH426-470ENGenes, Vol 12, Iss 1741, p 1741 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	cyanobacteria SSU (16S) rRNA phylogenomics sequencing workflow ribosomal proteins Genetics QH426-470
spellingShingle	cyanobacteria SSU (16S) rRNA phylogenomics sequencing workflow ribosomal proteins Genetics QH426-470 Luc Cornet Anne-Catherine Ahn Annick Wilmotte Denis Baurain ORPER: A Workflow for Constrained SSU rRNA Phylogenies
description	The continuous increase in sequenced genomes in public repositories makes the choice of interesting bacterial strains for future sequencing projects ever more complicated, as it is difficult to estimate the redundancy between these strains and the already available genomes. Therefore, we developed the Nextflow workflow “ORPER”, for “ORganism PlacER”, containerized in Singularity, which allows the determination the phylogenetic position of a collection of organisms in the genomic landscape. ORPER constrains the phylogenetic placement of SSU (16S) rRNA sequences in a multilocus reference tree based on ribosomal protein genes extracted from public genomes. We demonstrate the utility of ORPER on the Cyanobacteria phylum, by placing 152 strains of the BCCM/ULC collection.
format	article
author	Luc Cornet Anne-Catherine Ahn Annick Wilmotte Denis Baurain
author_facet	Luc Cornet Anne-Catherine Ahn Annick Wilmotte Denis Baurain
author_sort	Luc Cornet
title	ORPER: A Workflow for Constrained SSU rRNA Phylogenies
title_short	ORPER: A Workflow for Constrained SSU rRNA Phylogenies
title_full	ORPER: A Workflow for Constrained SSU rRNA Phylogenies
title_fullStr	ORPER: A Workflow for Constrained SSU rRNA Phylogenies
title_full_unstemmed	ORPER: A Workflow for Constrained SSU rRNA Phylogenies
title_sort	orper: a workflow for constrained ssu rrna phylogenies
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/916e9e17720f4201a57bd721580ee287
work_keys_str_mv	AT luccornet orperaworkflowforconstrainedssurrnaphylogenies AT annecatherineahn orperaworkflowforconstrainedssurrnaphylogenies AT annickwilmotte orperaworkflowforconstrainedssurrnaphylogenies AT denisbaurain orperaworkflowforconstrainedssurrnaphylogenies
_version_	1718412117851242496

ORPER: A Workflow for Constrained SSU rRNA Phylogenies

Ejemplares similares