ORPER: A Workflow for Constrained SSU rRNA Phylogenies.
Genes (Basel)
; 12(11)2021 10 29.
Article
em En
| MEDLINE
| ID: mdl-34828348
ABSTRACT
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.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Filogenia
/
Proteínas Ribossômicas
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Automação
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RNA Ribossômico 16S
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Cianobactérias
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Análise de Sequência de DNA
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Ribotipagem
Idioma:
En
Revista:
Genes (Basel)
Ano de publicação:
2021
Tipo de documento:
Article
País de afiliação:
Bélgica