SIV Barcode Pipeline

A simple snakemake pipeline to label, extract, and process the nanopore barcode data from the SIVmac239m2 virus.

Installation

Clone the repo repository repository and create a conda environment with the dependencies.

git clone https://github.com/DamLabResources/siv-barcode-pipeline.git
cd siv-barcode-pipeline
conda env create -f environment.yaml --prefix venv

Running the pipeline

If the data and the pipeline are in the same directory, you can run the pipeline with the following command:

snakemake --use-conda

If the data and the pipeline are not in the same directory, you can run the pipeline with the following command:

snakemake --use-conda -d $(DIREC)

Data

The raw reads should be organized as follows:

raw/
├── sample_1.bam
├── sample_2.bam
└── ...

After running the pipeline, the output will be organized as follows:

labeled/
├── sample_1.labeled.bam
├── sample_2.labeled.bam
└── ...

The metrics will be organized as follows:

metrics/
├── metrics/{sample}.extracted.metrics.yaml
├── metrics/{sample}.cellbc.metrics.yaml
├── metrics/{sample}.labeled.metrics.yaml
├── metrics/{sample}.sivmetrics.yaml
└── metrics/{sample}.depth.txt

A multiqc report will be generated in the report.html file.