Sphae: an automated toolkit for predicting phage therapy candidates from sequencing data.

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,

SUBMITTER: Papudeshi B 

PROVIDER: S-EPMC11783317 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature