its_classification

• Snakemake workflow to run RDP taxonomic classification on ITS FASTA sequences.
• based on honeypi

Requirements

• ASV FASTA from DADA2 or Qiime2.
• Pipelines
  • snakemake (required)
• Software
  • Conda (can be used together w/ snakemake) (required)
    • Conda
    • Miniconda
    • Anaconda

How to run

Install conda

• Do the following to install conda on neohuxley.

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod u+x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh

Clone the repository

• Download the GitHub repository.

git clone git@github.com:UKCEH-MolecularEcology/its_classification.git
cd its_classification

Create the conda environment

# create the environment
conda env create -f requirements.yaml

# Activate the environment
conda activate its_classifier

Set up the run

• Edit the config/config.yaml
• Following items in the config.yaml file need USER input
  • STEPS: run either 'rdp' or 'blast' or both as needed
  • amplicon_type: choose from ITS1 or ITS2
  • fasta: provide the path to the ASV FASTA file
  • data_dir and results_dir need to be provided
  • confidence: adjust the values as needed (between 0 to 1)

Running the workflow

# dry-run to check if everything is in order
snakemake -s workflow/Snakefile --configfile config/config.yaml --use-conda --cores 24 -rpn

# full run
snakemake -s workflow/Snakefile --configfile config/config.yaml --use-conda --cores 24 -rp