ArticleSTAR protocols2021
Protocol for post-processing of bacterial pangenome data using Pagoo pipeline.
Article in STAR protocols, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
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- Genomic Insights intoPathogens (Basel, Switzerland) · 2025Article
- Comparative genomics uncovers adaptive and biotechnological potential of Enterobacter xiangfangensis MDMC82 isolated from desert, and highlights putative core Enterobacteriaceae functions.Scientific reports · 2025Article
- Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth.PLoS biology · 2025Article
- Phylogenetic intermixing reveals stable fly-mediated circulation of mastitis-associated bacteria in dairy settings.mSystems · 2025Article
- Longitudinal survey investigating vectors and reservoirs forApplied and environmental microbiology · 2025Article
- Genomic characterization and comparative analysis of antibiotic resistance and virulence in Bangladeshi and global Klebsiella pneumoniae ST48 strains.Journal, genetic engineering & biotechnology · 2025Article
- Genomic Biosurveillance of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Biovar 3 Reveals Adaptation to Selective Pressures in New Zealand Orchards.Molecular plant pathology · 2025Article
- Decoding EcuadorianBiomedicines · 2025Article
- Pangenome analysis indicates evolutionary origins and genetic diversity: emphasis on the role of nodulation in symbioticFrontiers in plant science · 2025Article
- Article
- Population genetic analysis of clinicalFrontiers in cellular and infection microbiology · 2024Article
- Pangenome analysis provides insights into the genetic diversity, metabolic versatility, and evolution of the genusMicrobiology spectrum · 2023Article
- An antibiotic produced byFrontiers in microbiology · 2023Article
- Populational genomic insights ofFrontiers in microbiology · 2023Article
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2 authors.
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Abstract
Multiple downstream analyses are necessary to interpret the output of bacterial pangenome reconstruction software. This requires integrating diverse kinds of genetic and phenotypic data, which to date are left to each user's criterion. To fill this gap, we created Pagoo, a pangenome post-processing tool that leverages a standardized but flexible and extensible framework for data integration, analysis, and storage. Here, we provide the protocol for running Pagoo and performing from simple to more complex comparative analyses on bacterial pangenome data. For complete details on the use and execution of this protocol, please refer to Ferrés and Iraola (2021).
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