RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level.

Autor: Lamkiewicz K; RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, Jena, 07743, Germany., Barf LM; RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, Jena, 07743, Germany., Sachse K; RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, Jena, 07743, Germany., Hölzer M; Genome Competence Center (MF1), Robert Koch Institute, Berlin, 13353, Germany. hoelzerm@rki.de.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2024 Jul 01; Vol. 25 (1), pp. 170. Date of Electronic Publication: 2024 Jul 01.
DOI: 10.1186/s13059-024-03312-9
Abstrakt: Microbial pangenome analysis identifies present or absent genes in prokaryotic genomes. However, current tools are limited when analyzing species with higher sequence diversity or higher taxonomic orders such as genera or families. The Roary ILP Bacterial core Annotation Pipeline (RIBAP) uses an integer linear programming approach to refine gene clusters predicted by Roary for identifying core genes. RIBAP successfully handles the complexity and diversity of Chlamydia, Klebsiella, Brucella, and Enterococcus genomes, outperforming other established and recent pangenome tools for identifying all-encompassing core genes at the genus level. RIBAP is a freely available Nextflow pipeline at github.com/hoelzer-lab/ribap and zenodo.org/doi/10.5281/zenodo.10890871.
(© 2024. The Author(s).)
Databáze: MEDLINE
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