Sphae

Sphae streamlines the rapid genomic assessment of phage candidates to identify markers indicative of safety and efficacy for phage therapy.

Key Features:

• Automated quality control: Sphae integrates tools for quality control of sequencing data as part of its workflow.
• Genome assembly: Sphae performs assembly of phage genomes from sequencing data.
• Genome assessment: Sphae evaluates assembled phage genomes for therapeutic suitability.
• Genome annotation: Sphae annotates phage genomes with features tailored specifically for phage biology.
• Virulence factor detection: Sphae automates detection of virulence factors that could preclude therapeutic use.
• Antimicrobial resistance gene detection: Sphae identifies antimicrobial resistance genes in phage genomes.
• Lysogeny indicator detection: Sphae detects lysogeny indicators including integrase, recombinase, and transposase.
• Comprehensive reporting: Sphae outputs a comprehensive report enabling rapid assessment of phage safety and suitability.

Scientific Applications:

• Phage therapy candidate screening: Sphae rapidly assesses the therapeutic potential of phage candidates by identifying safety and efficacy markers.
• Genomic risk assessment: Sphae identifies genomic markers indicating potential risks such as toxins, antimicrobial resistance, or temperate lifecycle traits.
• Clinical phage deployment: Sphae expedites genomic evaluation to support rapid deployment of phages in clinical settings.

Methodology:

Sphae uses the Snakemake workflow manager to integrate tools for quality control, assembly, genome assessment, and annotation. The pipeline was benchmarked on 65 phage sequences.