ArticleGenome biology2024
RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Article
- Pangenome Dynamics and Functional Diversification in the Marine Genus Pseudoalteromonas: Association to Colony Pigmentation.Marine biotechnology (New York, N.Y.) · 2026Article
- Genome-Informed Identification of Species-Specific Diagnostic Markers for Listeria Using Pangenome Analysis.Pathogens (Basel, Switzerland) · 2026Article
- PyamilySeq: exposing the fragility of conventional gene (re)clustering and prokaryotic pangenomic inference methods.NAR genomics and bioinformatics · 2026Article
- Comparative genomics of space-resilientFEMS microbes · 2026Article
- Genomic Markers Distinguishing Shiga Toxin-ProducingPathogens (Basel, Switzerland) · 2025Article
- Linkage-based ortholog refinement in bacterial pangenomes with CLARC.Nucleic acids research · 2025Article
- Identification of Novel Gene-Specific Markers for Differentiating Various PathogenicPathogens (Basel, Switzerland) · 2025Article
- Exploring the genomic landscape of Chlamydiifrater species: novel features include multiple truncated major outer membrane proteins, unique genes and chlamydial plasticity zone orthologs.Access microbiology · 2025Article
- RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level.Genome biology · 2024Article
- Genomic analysis of 61 Chlamydia psittaci strains reveals extensive divergence associated with host preference.BMC genomics · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.