SCING: Single-Cell pIpeliNe Garden

Pronounced as "sing" /siŋ/

Unified framework for building and running single-cell computational pipelines

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Pipeline	Description	Version
SEQC	Single-cell & Single-nucleus RNA-seq 3' Preprocessor	0.2.11
SEQC Ada	SEQC AutomateD Analysis	0.0.4
Sharp (♯)	Demultiplexing Hashtag, CITE-seq, CellPlex, and ASAP-seq	0.1.1
Velopipe	RNA Velocity for SEQC	0.0.9
FastQC	A high throughput sequence QC analysis tool	0.11.9
Transgenes	Creating a reference package with transgenes	0.0.8
Cell Ranger GEX	Single-cell gene expression (3' and 5')	6.1.2
Cell Ranger V(D)J	Single-cell immune profiling (TCR/BCR)	6.1.2
Cell Ranger ATAC	Single-cell chromatin accessbility (ATAC)	2.1.0
Cell Ranger ARC	Single-cell multiome ATAC + Gene Expression	2.0.0
Space Ranger	Single-cell spatial gene expression	1.3.1
CellPlex	Cell multiplexing	6.1.2
mkref	Creating a human+mouse hybrid genome	0.0.6
ArchR	Processing and analyzing single-cell ATAC-seq data	0.1.0

Coming Soon

Pipeline	Description
Mito Tracing	Lineage tracing using mitochondrial mutations

Prerequisites

To use SCING, you need:

• Cromwell: a workflow management system for scientific workflows developed by the Broad Institute
• Amazon Web Services, Google Cloud Platform, Microsoft Azure, or HPC (with LSF, Slurm, ...)

If you need information about how to install Cromwell on Cloud/HPC, please follow the instructions below:

• Amazon Web Services
  • Amazon Genomics Workflow: https://github.com/hisplan/cromwell-gwf-setup
  • Amazon Genomics CLI (AGC): TBD
• Google Cloud Platform: TBD
• Microsoft Azure: TBD
• HPC with LSF: TBD

Install CLI (Command-Line Interface)

conda create -n scing python=3.8 pip
conda activate scing
git clone https://github.com/hisplan/scing.git
cd scing
pip install .

If you are a developer of SCING, additionally install either JRE or JDK. Here are some options for installing JRE or JDK:

JRE (Java 8 packaged by Cyclus):

conda install -c cyclus java-jre

JDK (Zulu OpenJDK v11):

conda install -c conda-forge openjdk

On HPC:

module add java/11.0.12

Build Containers

All the required docker containers are pre-built and publicly available/accessible via quay.io/hisplan, thus building the containers are optional. If you want to build the docker containers on your own and push them to your own docker registry, please follow the instructions here. Otherwise, skip to the Install section.

Install Pipelines

Run the following command to install all the pipelines:

scing install --config=config.yaml --home $HOME/scing/bin

Go to $HOME/scing/bin and extract everything:

cd $HOME/scing/bin
ls -1 *.tar.gz | xargs -I {} bash -c "tar xvzf {} && rm -rf {}"