/PipelineTypingOnly

Primary LanguagePython

PipelineTypingOnly

  • This script runs the post-assembly parts of the OLC Pipeline.

Requirements

Programs you'll need installed:

  • Quast (version 4.5)
  • blast
  • prodigal
  • NCBI ePCR
  • Python3

Python packages you'll need:

  • see requirements.txt (use pip3 install -r requirements.txt to install all)

Usage:

  • To run: python3 Typing.py -r <reference_file_path> <assembly_folder>
  • <reference_file_path> is where data files needed are stored. Currently at /mnt/nas/Adam/assemblypipeline/
  • <assembly_folder> is the path to a folder containing assemblies to be typed, in FASTA format. To be safe, use absolute, not relative paths.

More to come...