ArticleGenome biology2024
Efficient inference of large prokaryotic pangenomes with PanTA.
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 15 papers.
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Who cites it
15 citing papers in PubMed.
- How the social lives of bacteria affect their pangenome.Essays in biochemistry · 2026Review
- PanDelos-plus: A parallel algorithm for computing sequence homology in pangenomic analysis.PLoS computational biology · 2026Article
- Article
- De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping.Briefings in bioinformatics · 2026Article
- LSGFA: domain-based infraspecific large-scale prokaryotic genomic orthologous gene inference.BMC bioinformatics · 2026Article
- Species identification and genotyping ofMicrobiology spectrum · 2026Article
- Genotype-phenotype modeling of light ecotypes inbioRxiv : the preprint server for biology · 2026Article
- DEX: a consensus-based amino acid exchangeability measure for improved codon substitution modelling.bioRxiv : the preprint server for biology · 2026Article
- PyamilySeq: exposing the fragility of conventional gene (re)clustering and prokaryotic pangenomic inference methods.NAR genomics and bioinformatics · 2026Article
- GWAS and Machine Learning Screening of Genomic Determinants Underlying Host Adaptation in Swine and ChickenMicroorganisms · 2026Article
- PGAP2: A comprehensive toolkit for prokaryotic pan-genome analysis based on fine-grained feature networks.Nature communications · 2025Article
- How to measure bacterial genome plasticity? A novel index helps gather insights on pathogens.Microbial genomics · 2025Article
- Article
- Efficient inference of large prokaryotic pangenomes with PanTA.Genome biology · 2024Article
- AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance.BMC bioinformatics · 2024Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Pangenome inference is an indispensable step in bacterial genomics, yet its scalability poses a challenge due to the rapid growth of genomic collections. This paper presents PanTA, a software package designed for constructing pangenomes of large bacterial datasets, showing unprecedented efficiency levels multiple times higher than existing tools. PanTA introduces a novel mechanism to construct the pangenome progressively without rebuilding the accumulated collection from scratch. The progressive mode is shown to consume orders of magnitude less computational resources than existing solutions in managing growing datasets. The software is open source and is publicly available at https://github.com/amromics/panta and at 10.6084/m9.figshare.23724705 .
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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.