example

Example dataset

This is a very small, example dataset that should run on most machines.

Associated files:

example_config.yml

This file contains the configuration required for the pipeline. The pipeline needs paths to a sample list (below), where to save the output, and a .fasta-formatted target to align to.

all:
  output_dir: "output"
  sample_list: "example_samples.tsv"

align:
  target_fasta: "../reference/MN985325_1.fasta"

example_samples.yml

This file contains sample information in a tab-separated format. Paths to paired read files as well as information on the data collection strategy (e.g. long or short read sequencing) are included below.

sample_name	paired	method	r1	r2
paired1	True	short	data/paired1_r1.fastq.gz	data/paired1_r2.fastq.gz
paired2	True	long	data/paired2_r1.fastq.gz	data/paired2_r2.fastq.gz

To run starting from zero on a standard Linux/Ubuntu distro:

# setup conda

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p ${HOME}/miniconda3
export PATH=${PATH}:${HOME}/miniconda3/bin

# create environment and install dependencies through conda

conda create -n snakemake
conda activate snakemake
conda install snakemake=7.25.4 -c conda-forge -c bioconda

# download and run the pipeline on the test dataset

git clone https://github.com/louiejtaylor/frieman_genomes
cd example/
snakemake all_summarize --use-conda --conda-frontend conda -p --snakefile ../Snakefile --configfile example_config.yml --cores 1