/smartseq2_pipeline

A pipeline for processing single cell RNA-seq data generated with the SmartSeq2 protocol -- Now on nf-core: https://github.com/nf-core/smartseq2

Primary LanguageNextflowMIT LicenseMIT

nf-core/smartseq

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

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

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install with bioconda Docker

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
  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.

flowchart

Credits

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