GPHA: mpox kmer Typing

Info

• version: 0.1 (development)
• last updated (30.10.24)
• pathogen: mpox
• function:
• author: Deb
• summary: Repository containing code to rapidly identify the clade of mpox sequences using kmer typing.

Install

git clone https://gitlab.phe.gov.uk/gpha/analysis-and-evaluation/mpox_kmer_typing.git
cd mpox_kmer_typing
conda env create -n mpox_kmer_typing -f environment.yml
conda activate mpox_kmer_typing
pip install .

Install (For developers)

git clone https://gitlab.phe.gov.uk/gpha/analysis-and-evaluation/mpox_kmer_typing.git
cd mpox_kmer_typing
conda env create -n mpox_kmer_typing -f environment.yml
conda activate mpox_kmer_typing
pip install -e ".[dev]"
pytest . 

Description

This document contains the instructions on how to run the mpox kmer typing scan. This scan has been developed to rapidly identify mpox clades (I & II) basd on calculated kmer distances on both fasta & fastq file formats and for

• a) single sequences
• b) multiple-sequences

The scan has been packaged as container to allow for integration with CORE <name_of_pipeline> NEXTflow pipeline located on the SMED. In addition to it being able to still being used locally on user's personal device.

Modules

src
- analytics
  - kmer_typing_functions.py: application of kmer logic functions
  - processing.py: functions concerning the running of typing functions
- commands.py: contains argparse class relating to ingest and processing of terminal commands
- directories.py: functions concerning logic of selecting location and creation of sub-folders
- logfile.py: functions overwriting format of logging.py file
- mpox_kmer_typing.py: main file

Instructions

Usage

mpox_kmer_typing -t <["fastq", "fasta"]> -i <dir_input> -o: <dir_output} -r <refsketch>

• -t: type - specify input file type, ["fastq", "fasta"]
• -i: input - path to input file
• -o: output - output folder for results files
• -r: refsketch - path to reference sketch file