ArticlemSystems2022
MetaPhage: an Automated Pipeline for Analyzing, Annotating, and Classifying Bacteriophages in Metagenomics Sequencing Data.
Article in mSystems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 50 citations in OpenAlex.
- The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission.Nature communications · 2024Trial
- Artificial Intelligence in Bacteriophage Science: A Comprehensive Narrative Review of Applications, Challenges, and Translational Opportunities.Antibiotics (Basel, Switzerland) · 2026Review
- Prevalent gut phages encode modular adhesins mediating epithelial binding and endoplasmic reticulum trafficking.Nature communications · 2026Article
- Review
- The effects of bacteriophage cocktail treatment on healthy gut microbiota: anMicrobial genomics · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Article
- Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world.Briefings in bioinformatics · 2025Review
- Advanced Strategies in Phage Research: Innovations, Applications, and Challenges.Microorganisms · 2025Review
- Metagenomic investigation of viruses in green sea turtles (Frontiers in microbiology · 2025Article
- Diversity of DNA viruses in the atmosphere of sub-Antarctic South Georgia.Frontiers in microbiology · 2025Article
- Cave Pools in Carlsbad Caverns National Park Contain Diverse Bacteriophage Communities and Novel Viral Sequences.Microbial ecology · 2024Article
- Gastrointestinal jumbo phages possess independent synthesis and utilization systems of NADMicrobiome · 2024Article
- Sequencing-based analysis of microbiomes.Nature reviews. Genetics · 2024Review
- Article
- MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.mSystems · 2024Article
- Nanopore and Illumina sequencing reveal different viral populations from human gut samples.Microbial genomics · 2024Article
- Phage-inclusive profiling of human gut microbiomes with Phanta.Nature biotechnology · 2024Article
- Benchmarking informatics approaches for virus discovery: caution is needed when combiningmSystems · 2024Article
- Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study.Nature communications · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Phages are the most abundant biological entities on the planet, and they play an important role in controlling density, diversity, and network interactions among bacterial communities through predation and gene transfer. To date, a variety of bacteriophage identification tools have been developed that differ in the phage mining strategies used, input files requested, and results produced. However, new users attempting bacteriophage analysis can struggle to select the best methods and interpret the variety of results produced. Here, we present MetaPhage, a comprehensive reads-to-report pipeline that streamlines the use of multiple phage miners and generates an exhaustive report. The report both summarizes and visualizes the key findings and enables further exploration of key results via interactive filterable tables. The pipeline is implemented in Nextflow, a widely adopted workflow manager that enables an optimized parallelization of tasks in different locations, from local server to the cloud; this ensures reproducible results from containerized packages. MetaPhage is designed to enable scalability and reproducibility; also, it can be easily expanded to include new miners and methods as they are developed in this continuously growing field. MetaPhage is freely available under a GPL-3.0 license at https://github.com/MattiaPandolfoVR/MetaPhage.
Indexed as
Identifiers
What OpenQuestion holds
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.