nf-core/smartseq

Please use the version on nf-core: https://github.com/nf-core/smartseq2

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Preprocess scRNA-seq data generated with the SmartSeq2 protocol..

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.

Documentation

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