ORPER: A Workflow for Constrained SSU rRNA Phylogenies.

[en] 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.

Disciplines :

Biochemistry, biophysics & molecular biology
Genetics & genetic processes
Microbiology

Author, co-author :

Cornet, Luc ; Sciensano > BCCM/IHEM, Mycology and Aerobiology

Ahn, Anne-Catherine ; Université de Liège - ULiège > Département des sciences de la vie > Physiologie et génétique bactériennes

Wilmotte, Annick ; Université de Liège - ULiège > Département des sciences de la vie > Physiologie et génétique bactériennes

Baurain, Denis ; Université de Liège - ULiège > Département des sciences de la vie > Phylogénomique des eucaryotes

Language :

English

Title :

ORPER: A Workflow for Constrained SSU rRNA Phylogenies.

Publication date :

2021

Journal title :

Genes

ISSN :

2073-4425

Publisher :

Multidisciplinary Digital Publishing Institute (MDPI), Switzerland

Volume :

Issue :

Peer reviewed :

Peer Reviewed verified by ORBi

Tags :

CÉCI : Consortium des Équipements de Calcul Intensif

Additional URL :

https://www.mdpi.com/2073-4425/12/11/1741

Funders :

Politique Scientifique Fédérale (Belgique) - BELSPO
F.R.S.-FNRS - Fonds de la Recherche Scientifique [BE]
CÉCI - Consortium des Équipements de Calcul Intensif [BE]

Available on ORBi :

since 10 January 2022

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