- Installing the pipeline
- Preformating sequence library names
- Initial configuration & parameters
- Running snakefile
Installing the pipeline
I have now hosted all files on a public github project snakemake_16S_pipeline. The README file has information about installing everything, but essentially you need python3, miniconda, and snakemake.
First clone the github repository.
If everything worked, you should have a virtual environment named “snakemake_16S” that contains all necessary dependencies. To start it:
Preformating sequence library names
The pipeline assumes you have paired end libraries, which each sample pair in a different file. E.G. “sample1_R1_001.fastq.gz” The extensions can be changed in the config.yaml file.
You may wish to do some initial name cleaning before running the pipeline. E.G. I changed my sample names from WAO_T0C1_S112_L001_R1_001.fastq.gz to WAO_T0C1_R1_001_fastq.gz
Initial configuration & parameters
Check out the config.yaml file. Here you can specify specifics for your sample set. Change the paths for: read_directory: chimera_db:
You may want to change the threads to match your system.
The oligos file should be in the “additional_files” directory, but you can change this path if you need to.
To start the pipeline simply type:
If you’d like to run the pipeline with some steps in parallel, specify the number of threads available with: