ArticleBioinformatics (Oxford, England)2023
Pharokka: a fast scalable bacteriophage annotation tool.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 428 papers.
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Who cites it
428 citing papers in PubMed.
- Microbiota-constrained bacterial density limits phage infection in the gut and allows persistence of susceptible cells.iScience · 2026Article
- A rationally constructed phage cocktail effectively enhances antibacterial activity against Salmonella Enteritidis in chickens.Veterinary research communications · 2026Article
- Complete genome sequence ofMicrobiology resource announcements · 2026Article
- Complete genome sequences of bacteriophages active against multidrug-resistantMicrobiology resource announcements · 2026Article
- Article
- Members of theMicrobial genomics · 2026Article
- Farm-adapted multicomponent bacteriophage preparation for environmental biocontrol in commercial dairy cattle housing: A One Health approach.Veterinary world · 2026Article
- Harnessing phage-ciprofloxacin synergy to overcome multidrug-resistant infections and biofilm persistence.Archives of microbiology · 2026Article
- Smaller Genomes and Shorter Prophage Sequences Differentiate Clinical from Environmental Isolates ofbioRxiv : the preprint server for biology · 2026Article
- Characterization of Novel Mycobacteriophages of Subcluster A3: Evolutionary Plasticity of the Lysogeny Module and Lytic Potential.International journal of molecular sciences · 2026Article
- Characterization of vaginal lactobacilli from South African women toward the development of a biotherapeutic to optimize the vaginal microbiome.Applied and environmental microbiology · 2026Article
- Cervicovaginal Virome Restructuring Associated with HPV Status, Bacterial Dysbiosis, and Cervical Cytological Abnormalities.Viruses · 2026Article
- Distinct Evolutionary Selection Patterns in Temperate and Filamentous Phages of Phocaeicola vulgatus in Health and IBD.Research square · 2026Article
- Phage Genomics and Bioinformatics in Therapeutic Development: Evidence Limits, Validation Gates, and Translational Decision-Making.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Biocontrol potential and genomic analysis of novel lytic bacteriophage CABI-SEA 2302 against multidrug-resistant avian pathogenic Escherichia coli associated with colibacillosis.Poultry science · 2026Article
- Genome sequences of sixMicrobiology resource announcements · 2026Article
- Isolation and genomic characterization of bacteriophage Vanta, a lyticMicrobiology resource announcements · 2026Article
- Isolation and genomic characterization of bacteriophage Luminis, a lyticMicrobiology resource announcements · 2026Article
- Bacteriophages Control Epiphytic Pseudomonas syringae Populations in Highbush Blueberry Leaves.Microbial biotechnology · 2026Article
- Colibactin produced by a honeybee gut symbiont mediates pathogen defence.Nature microbiology · 2026Article
368 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
summaryIn recent years, there has been an increasing interest in bacteriophages, which has led to growing numbers of bacteriophage genomic sequences becoming available. Consequently, there is a need for a rapid and consistent genomic annotation tool dedicated for bacteriophages. Existing tools either are not designed specifically for bacteriophages or are web- and email-based and require significant manual curation, which makes their integration into bioinformatic pipelines challenging. Pharokka was created to provide a tool that annotates bacteriophage genomes easily, rapidly and consistently with standards compliant outputs. Moreover, Pharokka requires only two lines of code to install and use and takes under 5 min to run for an average 50-kb bacteriophage genome. AVAILABILITY AND IMPLEMENTATION: Pharokka is implemented in Python and is available as a bioconda package using 'conda install -c bioconda pharokka'. The source code is available on GitHub (https://github.com/gbouras13/pharokka). Pharokka has been tested on Linux-64 and MacOSX machines and on Windows using a Linux Virtual Machine.
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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.