gongyh/scgs repository overview

⁠gongyh/nf-core-scgs

Single Cell Genome Sequencing data analysis pipeline.

⁠Introduction

The pipeline is used for single cell genome sequencing data analysis and built using Nextflow⁠, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker / singularity containers making installation trivial and results highly reproducible.

⁠Quick start

Prerequisites: Git, Java 8 or later, Docker

## Install Nextflow
$ curl -s https://get.nextflow.io | bash
## Pull docker container
$ docker pull quay.io/gongyh/nf-core-scgs:v1.1
## Get the pipeline
$ git clone -b v1.1 https://github.com/gongyh/nf-core-scgs.git
## Test (16 cpu cores, 48G memory)
$ ./nextflow run nf-core-scgs -profile test_local,docker

⁠Documentation

The gongyh/nf-core-scgs pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation⁠
2. Pipeline configuration
   • Local installation⁠
   • Adding your own system⁠
   • Reference genomes⁠
3. Running the pipeline⁠
4. Output and how to interpret the results⁠
5. Troubleshooting⁠

⁠Related publications

[1] Xu, T., Gong, Y., Su, X., Zhu, P., Dai, J., Xu, J., Ma, B., Phenome-Genome Profiling of Single Bacterial Cell by Raman-Activated Gravity-Driven Encapsulation and Sequencing. Small 2020, 2001172. https://doi.org/10.1002/smll.202001172⁠ Details⁠

[2] Su, X., Gong, Y., Gou, H., Jing, X., Xu, T., Zheng, X., Chen, R., Li, Y., Ji, Y., Ma, B., Xu, J., Rational Optimization of Raman-Activated Cell Ejection and Sequencing for Bacteria. Analytical Chemistry, 2020. https://doi.org/10.1021/acs.analchem.9b05345⁠

⁠Contact

gongyh/nf-core-scgs is maintained by Yanhai Gong⁠. We look forward to receive your feedback, bug reports, or suggestions for the further development of this pipeline.

⁠License

This pipeline is open source under the MIT license, and integrates wonderful third-party softwares, which remain owned and copyrighted by their respective developers. Authors cannot be held legally or morally responsible for any consequences that may arise from using or misusing it.