This repository contains a collection of pipelines that aid the analysis of single cell sequencing experiments. Currently there is one pipeline implimented that allows the analysis of drop-seq and 10X sequencing analysis. Current pipelines in development: 1) pseudoalignment scpipeline 2) velocyto pipeline 2) kallisto bustools pipeline.
The preferred method for installation is through conda/mamba as a separate environment:
(Optional) # Create a new folder in your desired location and cd into it:
mkdir scflow_install && cd scflow_install
# Install the scflow package:
git clone [email protected]:cribbslab/scflow.git
mamba env create -f scflow/conda/environments/scflow.yml
conda activate scflow
cd scflow
python setup.py develop
# Install a modified version of kb-tools from Adam's cloned repo:
git clone [email protected]:Acribbs/kb_python.git
cd kb_python
python setup.py develop
# Check that the installation has worked:
scflow --help
Run the scflow --help command view the help documentation for how to run the single-cell repository.
To run the main single_cell droplet based pipeline run first generate a configuration file::
scflow singlecell config
Then run the pipeline::
scflow singlecell make full -v5
Then to run the report::
scflow singlecell make build_report
Further help that introduces single-cell and provides a tutorial of how to run example code can be found at read the docs