nfcore/scrnaseq repository overview

A fully automated Nextflow pipeline for Droplet-based (e.g. 10x Genomics) single-cell RNA-Seq data.

⁠Introduction

nf-core/scrnaseq is a bioinformatics best-practise analysis pipeline for

The pipeline is built using Nextflow⁠, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

This is a community effort in building a pipeline capable to support:

• Alevin + AlevinQC
• STARSolo
• Kallisto + BUStools

⁠Pipeline Summary

By default, the pipeline currently performs the following:

• Sequencing quality control (FastQC)
• Overall pipeline run summaries (MultiQC)

⁠Documentation

The nf-core/scrnaseq pipeline comes with documentation about the pipeline: usage⁠ and output⁠.

⁠Credits

The nf-core/scrnaseq was initiated by Peter J. Bailey⁠ (Salmon Alevin, AlevinQC) with major contributions from Olga Botvinnik⁠ (STARsolo, Testdata) and Alex Peltzer⁠ (Kallisto/BusTools workflow).

We thank the following people for their extensive assistance in the development of this pipeline:

⁠Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines⁠.

For further information or help, don't hesitate to get in touch on the Slack #scrnaseq channel⁠ (you can join with this invite⁠).

⁠Citations

The basic benchmarks that were used as motivation for incorporating the three available modular workflows can be found in this publication⁠.

We offer all three paths for the processing of scRNAseq data so it remains up to the user to decide which pipeline workflow is chosen for a particular analysis question.

You can cite the nf-core publication as follows: