nf-core/smartseq2

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Introduction

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.

Quick Start

i. Install nextflow

ii. Install either Docker or Singularity for full pipeline reproducibility (please only use Conda as a last resort; see docs)

iii. Download the pipeline and test it on a minimal dataset with a single command

nextflow run nf-core/smartseq2 -profile test,<docker/singularity/conda/institute>

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 docker or singularity and set the appropriate execution settings for your local compute environment.

iv. Start running your own analysis!

nextflow run nf-core/smartseq2 -profile <docker/singularity/conda/institute> --reads '*_R{1,2}.fastq.gz' --genome GRCh37

See usage docs for all of the available options when running the pipeline.

Documentation

The nf-core/smartseq2 pipeline comes with documentation about the pipeline, found in the docs/ directory:

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

This pipeline was developed to process single cell RNA-seq data generated using the Smart-Seq2 protocol.

The pipeline features:

• Quality control using fastqc and multiqc
• Alignment using STAR
• Quantification using rsem or featureCounts
• TCR analysis using TraCeR.
• BCR analysis using BraCeR.

Credits

nf-core/smartseq2 was originally written by Sandro Carollo, Giorgos Fotakis and Gregor Sturm

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 Slack (you can join with this invite).

Citation

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. ReadCube: Full Access Link