PRANCc

: a Pipeline Researching AMR, Neisseria spp., and CRISPR correlations v0.3.2-beta

Copyright (C) 2023, 2024-2025 Tyler Hall, Samantha J. Webster

PRANCc is a pipeline in progress to find and identify cas genes and CRISPR-Cas systems using a variety of isolatable tools, primarily CrisprCasFinder, CrisprCasTyper, CRISPRIdentify and CRISPRDetect as modified and installed through PADLOC and output compiled results as a way of analysing large numbers of sequences as well as identifying anti-microbial resistance (AMR) genes using PADLOC from whole genome sequences (WGS). Then, using that information, running statistical analyses to find relationships between the two.

This project was started with data from Pathogenwatch and uses the collected metadata as well as inferred AMR types/NG Star data to verify detected genes. Using that metadata we can also conduct analyses on geographic spread, patterns over time and from sexual behaviour of the hosts.

We went on to use NCBI, as well as the input of Makarova et al 2018 to test efficacy between tools.

Installation

To install, install the prerequisites, or ask your system admin to. workflow/install/awsinstall.sh is how I installed these prereqs, but that script is provided as-is and is Ubuntu/Debian specific. For compatibility reasons, it's best to install this on a clean slate. Due to the HMM model requirements of CRISPRIdentify, this installer will download about 1GB.

Installs

• CrisprCasFinder (into Conda environment 'crisprcasfinder')
  • MacSyFinder
  • CasFinder
• PADLOC (into Conda environment 'padloc')
  • CrisprDetect
• CrisprCasTyper
• CRISPRIdentify
• gdown
• the various prereqs of those programs

Prerequisites

• Linux
• Conda
• Mamba
  • (I recommend installing Miniforge which includes both Conda and Mamba. You can find it at https://github.com/conda-forge/miniforge)
• Snakemake
• build-essential (or your Linux flavour of make, if not installed by default)

Setup

1. Download and extract this repository
2. Make sure the preequisites are installed and ready to use (make sure Conda and Mamba are initialised, particularly!)
3. Run workflow/install/install_prancc.sh
4. You're done!

Run

1. Add all the .fna files you want to analyse to the prancc/upload folder
2. Activate the snakemake environment (if you used my install script, conda activate snakemake)
3. Navigate inside the PRANCc folder that was extracted
4. snakemake --cores all --use-conda

See https://snakemake.readthedocs.io/en/v5.1.4/executable.html for more information about executing snakemake workflows.

Output

Produces a tarball results.tar.gz in the prancc folder containing:

• The raw output of:
  • CrisprCasFinder
  • CrisprCasTyper
  • CRISPRIdentify
  • CrisprDetect
  • PADLOC
• .tsv sheets of the summarised output of:
  • CrisprCasFinder (crispr and cas)
  • CrisprCasTyper
  • CRISPRIdentify
  • PADLOC
  • version logs of all environments and conda

Contact us

If you have any questions, please feel free to contact us! You can reach me, Tyler, at avcloudy@gmail.com, or both of us at delbeauxlab@gmail.com. This is very much a work in progress!