Swiss TPH PhiP-Seq

This repository contains the input and output directories associated with this github repository. Together, they consitute and document a snakemake workflow to construct a PhiP-Seq oligo library from downloaded fasta files. This is version 1 (created in March 2026), targeting several pathogenic Borrelia species, TBEV, Dengue and Rickettsie helvetica. Input.zip contains all fasta sequences used to construct the oligo library. It serves as the input for the snakemake workflow documented here. Most input sequences are results of uniprot queries, however several entries were taken over from Anahtar et al., 2025. Results.zip contains all intermediate and the final result of the library construction done by the snakemake workflow documented here.