- Copy the files and directories from the repository to the project directory where the examples are located.
root
|
|_ [PROJECT_NAME]
|
|_ Sample_RXxxxx1
|_ Sample_RXxxxx2
|_ ....
|_ ....
|_ envs
|_ source
|_ ref
|_ config.yaml
|_ twist_sars_cov2.bed
|_ Snakefile_UMI
|_ Snakefile_Twist
|_ kraken
|_ kraken2_human
- Download kraken database
wget https://zenodo.org/record/3738199/files/kraken2_human.tar.gz
- Extract it
tar -xvzf kraken2_human.tar.gz
- Configure the config.yaml file
samples: 'RXxxxx1,RXxxxx2' # list of samples without "Sample_"
target_twist: '/path/to/twist_sars_cov2.bed' # e.g: /root/[PROJECT_NAME]/twist_sars_cov2.bed
reference: '/path/to/ref/MN908947.3.fasta' # e.g: /root/[PROJECT_NAME]/ref/MN908947.3.fasta
adapter1: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCA' # Adapter read 1
adapter2: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT' # Adapter read 2
krakendb: '/root/kraken/kraken2_human' # extracted kraken path
threads: 8 # number of threads
- running snakefile
cd [PROJECT_NAME]
snakemake -s Snakefile_UMI --configfile config.yaml --cores
or
snakemake -s Snakefile_Twist --configfile config.yaml --cores
- Recommended: running snakemake from mamba enviroment
mamba create -c conda-forge -c bioconda -n snakemake snakemake
mamba activate snakemake