A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol.
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.
iii. Download the pipeline and test it on a minimal dataset with a single command
Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use
-profile <institute>in your command. This will enable either
singularityand set the appropriate execution settings for your local compute environment.
iv. Start running your own analysis!
See usage docs for all of the available options when running the pipeline.
The nf-core/smartseq2 pipeline comes with documentation about the pipeline, found in the
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
This pipeline was developed to process single cell RNA-seq data generated using the Smart-Seq2 protocol.
The pipeline features:
- Quality control using
- Alignment using
- Quantification using
- TCR analysis using
- BCR analysis using
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
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.