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Welcome

Welcome to the ARPEGGIO wiki! Here you can find a step-by-step guide on how to set up ARPEGGIO. Please use the Wiki index below to find details about the different steps required to run ARPEGGIO.

Quick install & start

To use ARPEGGIO you need to install Snakemake via Conda. Once everything is set up, run the following commands to clone the ARPEGGIO repository to your computer and run the workflow with a test dataset. (Note: the first time might take a while to create the environments)

git clone https://github.com/supermaxiste/ARPEGGIO
cd ARPEGGIO
snakemake --use-conda

Wiki index

Basic steps to run & get an idea of the workflow:

1. Overview
2. Input files
3. Configuration file
4. Running Snakemake
5. Output structure

Advanced information to better understand & modify the workflow:

6. Snakefile (rules and relationships)
7. Scripts
8. Software and tools