A single-cell RNAseq pipeline for 10X genomics data
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
- Kallisto + BUStools
By default, the pipeline currently performs the following:
- Sequencing quality control (
- Overall pipeline run summaries (
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.
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:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.