ArticleBioinformatics advances2025
Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data.
Article in Bioinformatics advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- Strain-level molecular and infection traits are associated with differences in phage efficacy against Pseudomonas aeruginosa.Scientific reports · 2026Article
- Progress of Bacteriophage Research and Application in the Treatment of Bovine Mastitis: A Review.Veterinary sciences · 2026Review
- Bacteriophage-Based Therapeutic, Diagnostic, and Biocontrol Platforms: Engineering, Evidence, and Translational Challenges.International journal of molecular sciences · 2026Review
- The epidermal ecotone: a proposed model system for marine viral ecology at the animal-environmental interface.NPJ biofilms and microbiomes · 2026Review
- Electrospun Phage-Loaded Bilayer Nanofibrous Scaffolds for Wound Dressing Applications: A Comparative Study of Different Bacteriophages.Journal of functional biomaterials · 2026Article
- Protein structure-informed bacteriophage genome annotation with Phold.Nucleic acids research · 2026Article
- The Role of Genomics in Advancing and Standardising Bacteriophage Therapy.Antibiotics (Basel, Switzerland) · 2026Review
- Article
- Phage isolation and functional characterization reveal strong antibiofilm activity againstFrontiers in cellular and infection microbiology · 2026Article
- Computational function prediction of bacteria and phage proteins.Microbiology and molecular biology reviews : MMBR · 2025Review
- Revisiting phage tail spike architecture: evidence for undetected receptor-binding proteins inFrontiers in microbiology · 2025Article
Corrections and comments
- Update of
Authors and funding
18 authors.
Funding
Abstract
Motivation: Phage therapy offers a viable alternative for bacterial infections amid rising antimicrobial resistance. Its success relies on selecting safe and effective phage candidates that require comprehensive genomic screening to identify potential risks. However, this process is often labor intensive and time-consuming, hindering rapid clinical deployment. Results: We developed Sphae, an automated bioinformatics pipeline designed to streamline the therapeutic potential of a phage in under 10 minutes. Using Snakemake workflow manager, Sphae integrates tools for quality control, assembly, genome assessment, and annotation tailored specifically for phage biology. Sphae automates the detection of key genomic markers, including virulence factors, antimicrobial resistance genes, and lysogeny indicators such as integrase, recombinase, and transposase, which could preclude therapeutic use. Among the 65 phage sequences analyzed, 28 showed therapeutic potential, 8 failed due to low sequencing depth, 22 contained prophage or virulent markers, and 23 had multiple phage genomes. This workflow produces a report to assess phage safety and therapy suitability quickly. Sphae is scalable and portable, facilitating efficient deployment across most high-performance computing and cloud platforms, accelerating the genomic evaluation process. Availability and implementation: Sphae source code is freely available at https://github.com/linsalrob/sphae, with installation supported on Conda, PyPi, Docker containers.
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.