ArticleMolecular biology and evolution2021
CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- MetaStrainer: accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.Bioinformatics (Oxford, England) · 2026Article
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- Prevalence and Evolutionary Implications of Genome Rearrangements in Bacteria.Genome biology and evolution · 2026Article
- Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy.Nature communications · 2025Article
- Homologous recombination shapes the architecture and evolution of bacterial genomes.Nucleic acids research · 2025Article
- Pangenome analysis indicates evolutionary origins and genetic diversity: emphasis on the role of nodulation in symbioticFrontiers in plant science · 2025Article
- Applying the Classic Test dN/dS to Detect Selection in Archaea.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria.Molecular biology and evolution · 2024Article
- Homologous Recombination Shapes the Architecture and Evolution of Bacterial Genomes.bioRxiv : the preprint server for biology · 2024Article
- Evolution of homologous recombination rates across bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Outbreak investigation of Serratia marcescens bloodstream infection in an obstetric ward for high-risk pregnant women.BMC infectious diseases · 2024Article
- Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses.Genome biology · 2023Article
- Characterization and description of Gabonibacter chumensis sp. nov., isolated from feces of a patient with non-small cell lung cancer treated with immunotherapy.Archives of microbiology · 2023Article
- Widespread extinctions of co-diversified primate gut bacterial symbionts from humans.Nature microbiology · 2023Article
- Gene flow and introgression are pervasive forces shaping the evolution of bacterial species.Genome biology · 2022Article
- Article
- Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales.PLoS genetics · 2022Article
- Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth.The ISME journal · 2022Article
- Phylogenetic systematics ofMicrobial genomics · 2021Article
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Authors and funding
4 authors.
Funding
Abstract
The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. Inferring the core genome is integral to many genomic analyses, however, most methods rely on the comparison of all the pairs of genomes; a step that is becoming increasingly difficult given the massive accumulation of genomic data. Here, we present CoreCruncher; a program that robustly and rapidly constructs core genomes across hundreds or thousands of genomes. CoreCruncher does not compute all pairwise genome comparisons and uses a heuristic based on the distributions of identity scores to classify sequences as orthologs or paralogs/xenologs. Although it is much faster than current methods, our results indicate that our approach is more conservative than other tools and less sensitive to the presence of paralogs and xenologs. CoreCruncher is freely available from: https://github.com/lbobay/CoreCruncher. CoreCruncher is written in Python 3.7 and can also run on Python 2.7 without modification. It requires the python library Numpy and either Usearch or Blast. Certain options require the programs muscle or mafft.
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