seekdeep_analysis_snakemake

This repository is attempting to be a general purpose seekdeep analysis pipeline. Outputs include:

• total read counts for every sample as a table
• total read counts for every sample as a heatmap
• complexity of infection (number of haplotypes per sample) as a table
• complexity of infection (number of haplotypes per sample) as a heatmap
• if applicable, relative abundance of amino acid point mutations as a table
• if applicable, relative abundance of amino acid point mutations as a heatmap

Installation:

• Install conda: https://github.com/conda-forge/miniforge#mambaforge
• Create a conda environment and install snakemake there:

conda create -c conda-forge -c bioconda -n snakemake snakemake

Setup your environment:

• Change directory to a folder where you want to run the analysis
• Download the analyze_seekdeep.smk file into this folder (e.g. with git clone)
• Download the analyze_seekdeep.yaml file into same folder (e.g. git clone)

Usage:

• Edit the config.yaml file using the instructions in the comments. Use a text editor that outputs unix line endings (e.g. vscode, notepad++, gedit, micro, emacs, vim, vi, etc.)
• If snakemake is not your active conda environment, activate snakemake with:

conda activate snakemake

• Run snakemake with:

snakemake -s analyze_seekdeep.smk --cores [your_desired_core_count]