A single-cell RNAseq pipeline for 10X genomics data
nf-core/scrnaseq is a bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data.
This is a community effort in building a pipeline capable to support:
- Alevin-Fry + AlevinQC
- Kallisto + BUStools
First, prepare a samplesheet with your input data that looks as follows:
Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
Now, you can run the pipeline using:
Please provide pipeline parameters via the CLI or Nextflow
-params-file option. Custom config files including those
provided by the
-c Nextflow option can be used to provide any configuration except for parameters;
Decision Tree for users
The nf-core/scrnaseq pipeline features several paths to analyze your single cell data. Future additions will also be done soon, e.g. the addition of multi-ome analysis types. To aid users in analyzing their data, we have added a decision tree to help people decide on what type of analysis they want to run and how to choose appropriate parameters for that.
Options for the respective alignment method can be found here to choose between methods.
To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.
nf-core/scrnaseq was originally written by Bailey PJ, Botvinnik O, Marques de Almeida F, Gabernet G, Peltzer A, Sturm G.
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.
If you use nf-core/scrnaseq for your analysis, please cite it using the following doi: 10.5281/zenodo.3568187
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.
An extensive list of references for the tools used by the pipeline can be found in the