Pan Salmonella phages degenerate PCR primers design

This is the repository for supplementary materials for the upcoming publication

Files:

• 📑 01_PanACoTA_journal.ipynb - laboratory journal with commands to reproduce the 1st step of pipeline
• 📑 02_Pangenome_vis_journal.R - laboratory journal with commands to reproduce the 2nd step of pipeline
• 📑 03_phylo_journal.R - laboratory journal with commands to reproduce the 3rd step of pipeline
• 📑 04_DECIPHER_journal.R - laboratory journal with commands to reproduce the 4th step of pipeline
• 📑 panacota.yaml - conda environment
• 📁 scripts - folder with scripts:
  • 📑 filter_seqs.py - script that filters out "trash" downloaded from RefSeq with Entrez
  • 📑 sepfasta.py - script that separates 1 fasta with multiple seqs to multiple fasta files with 1 seq
  • 📑 process_LSTINFO.py - script that filters PanACoTA's corepers subcommand output to make it fit align subcommand

Instruction:

• Create new environment panacota

conda env create -f panacota.yaml

Pipeline:

Figure 1. Pipeline overview.