ArticleGenome research2023
Accurate and fast graph-based pangenome annotation and clustering with ggCaller.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 27 citations in OpenAlex.
- Interrogating the Escherichia coli Epitranscriptome Via CRISPR Interference and Nanopore Native RNA Sequencing.MicrobiologyOpen · 2026Article
- A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions.Genome medicine · 2026Article
- RefiningMicrobial genomics · 2026Article
- A versatile multi-components mixed model for bacterial-Genome Wide association studies.Nature communications · 2026Article
- Comprehensive characterization and genome-resolved insights into the probiotic potential of Bacillus sp. KNSH39 isolated from Litopenaeus vannamei intestine.World journal of microbiology & biotechnology · 2026Article
- Hidden in the Pangenome? Machine Learning-Driven Discovery of Antimicrobial Potential inBioinformatics and biology insights · 2026Article
- Pangenomics in the Mimulus guttatus Species Complex.Molecular ecology resources · 2026Article
- Multiscale comparative pathogenomic analysis of Vibrio anguillarum linking serotype diversity, genomic plasticity and pathogenicity.Journal, genetic engineering & biotechnology · 2025Article
- Linkage-based ortholog refinement in bacterial pangenomes with CLARC.Nucleic acids research · 2025Article
- Pathogenomic Insights intoAnimals : an open access journal from MDPI · 2025Article
- Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm.Genome research · 2025Article
- Article
- Quantifying the Evolutionary Dynamics of Structure and Content in Closely Related E. coli Genomes.Molecular biology and evolution · 2025Article
- Beyond H37Rv:Frontiers in microbiology · 2025Review
- Benchmarking pangenome dynamics and horizontal gene transfer inFrontiers in microbiology · 2025Article
- Genomic Characterization ofMicroorganisms · 2024Article
- A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study.BMC genomics · 2024Review
- Genome-resolved metagenomics: a game changer for microbiome medicine.Experimental & molecular medicine · 2024Review
- Decoding huge phage diversity: a taxonomic classification of Lak megaphages.The Journal of general virology · 2024Article
- Unveiling the whole genomic features and potential probiotic characteristics of novelFrontiers in microbiology · 2024Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Bacterial genomes differ in both gene content and sequence mutations, which underlie extensive phenotypic diversity, including variation in susceptibility to antimicrobials or vaccine-induced immunity. To identify and quantify important variants, all genes within a population must be predicted, functionally annotated, and clustered, representing the "pangenome." Despite the volume of genome data available, gene prediction and annotation are currently conducted in isolation on individual genomes, which is computationally inefficient and frequently inconsistent across genomes. Here, we introduce the open-source software graph-gene-caller (ggCaller). ggCaller combines gene prediction, functional annotation, and clustering into a single workflow using population-wide de Bruijn graphs, removing redundancy in gene annotation and resulting in more accurate gene predictions and orthologue clustering. We applied ggCaller to simulated and real-world bacterial data sets containing hundreds or thousands of genomes, comparing it to current state-of-the-art tools. ggCaller has considerable speed-ups with equivalent or greater accuracy, particularly with data sets containing complex sources of error, such as assembly contamination or fragmentation. ggCaller is also an important extension to bacterial genome-wide association studies, enabling querying of annotated graphs for functional analyses. We highlight this application by functionally annotating DNA sequences with significant associations to tetracycline and macrolide resistance in
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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.