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Workflow to conduct preliminary pop gen analysis from individual whole genome sequencing

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Snakemake Population Genetics Workflow

This workflow collects several of the necessary steps to perform a pop gen analysis with individual genomes. There are three main files that are required to use this workflow:

  1. A parameter config file: a samples is located in config/parameters.yaml. Adjust the parameters in accourdance with your systems available resources.
  2. A sample metadata file: an example can be found in test/samples.csv.
  3. individual fastq files: This files can be store anywhere where you can have write and read access within the system. Just remember to add the location in the sample metadata file.

Running the workflow:

Installation of required software:

Ensure all require tools and are installed correctly:

Testing the workflow:

Generating a DAG graphs for the workflow

To run the DAG graph do:

snakemake --dag --use-conda -c all -s Snakefile | dot -Tpdf > ./fig/DAG.pdf

To make a filegraph with details of inputs and outputs (my prefered option)

snakemake --filegraph --use-conda -c all -s Snakefile | dot -Tpdf > ./fig/simple-filegraph-local-rules.pdf

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