ArticleBioinformatics (Oxford, England)2023
Phables: from fragmented assemblies to high-quality bacteriophage genomes.
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 39 papers.
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Who cites it
39 citing papers in PubMed, 43 citations in OpenAlex.
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- ViralQC: a tool for assessing completeness and contamination of predicted viral contigs.Bioinformatics (Oxford, England) · 2026Article
- High-quality phage assembly from metagenomes with PALACE.Nature biotechnology · 2026Article
- Decoding Viral Dark Matter: Metagenomic Prokaryotic Virus Characterization With Pharokka, Phold, and Phynteny.Current protocols · 2026Article
- Ten quick tips for classifying unknown bacteriophage.PLoS computational biology · 2026Article
- Co-migration of hundreds of microbial species over metres drives selection and promotes non-motile hitchhikers.Nature communications · 2026Article
- Virome datasets and viral metagenome-assembled genomes from aquaculture-impacted freshwater environments.Scientific data · 2026Article
- Diversity and prevalence of dairy streptococcal phages in two European dairy fermentation facilities over a one-year period.Microbial genomics · 2026Article
- Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages.NPJ biofilms and microbiomes · 2026Article
- Characterization and evaluation of a phage cocktail targeting Salmonella enterica in a Turkey farm.BMC microbiology · 2026Article
- piqtree: a python package for seamless phylogenetic inference with IQ-TREE.Molecular biology and evolution · 2026Article
- Picobirnavirus: how do you find where it's hiding?Critical reviews in microbiology · 2026Review
- The epidermal ecotone: a proposed model system for marine viral ecology at the animal-environmental interface.NPJ biofilms and microbiomes · 2026Review
- Gut virome dynamics: from commensal to critical player in health and disease.Nature reviews. Gastroenterology & hepatology · 2026Review
- Bacteriophages in gut metagenomes: from analysis to application.Virology journal · 2026Review
- Protein structure-informed bacteriophage genome annotation with Phold.Nucleic acids research · 2026Article
- Article
- Computational Microbial and Viral Ecology Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- PBIP: a deep learning framework for predicting phage-bacterium interactions at the strain level.Briefings in bioinformatics · 2025Article
- Distinct shifts in bacteriophage diversity and abundance during various stages of Gouda-type cheese production.Applied and environmental microbiology · 2025Article
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Authors and funding
12 authors at 2 institutions in 2 countries.
Funding
Abstract
motivationMicrobial communities have a profound impact on both human health and various environments. Viruses infecting bacteria, known as bacteriophages or phages, play a key role in modulating bacterial communities within environments. High-quality phage genome sequences are essential for advancing our understanding of phage biology, enabling comparative genomics studies and developing phage-based diagnostic tools. Most available viral identification tools consider individual sequences to determine whether they are of viral origin. As a result of challenges in viral assembly, fragmentation of genomes can occur, and existing tools may recover incomplete genome fragments. Therefore, the identification and characterization of novel phage genomes remain a challenge, leading to the need of improved approaches for phage genome recovery.
resultsWe introduce Phables, a new computational method to resolve phage genomes from fragmented viral metagenome assemblies. Phables identifies phage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic samples obtained from different environments show that Phables recovers on average over 49% more high-quality phage genomes compared to existing viral identification tools. Furthermore, Phables can resolve variant phage genomes with over 99% average nucleotide identity, a distinction that existing tools are unable to make. AVAILABILITY AND IMPLEMENTATION: Phables is available on GitHub at https://github.com/Vini2/phables.
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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.