Please use the version on nf-core: https://github.com/nf-core/smartseq2
Preprocess scRNA-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.
The nf-core/smartseq pipeline comes with documentation about the pipeline, found in the docs/
directory:
- Installation
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- 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
andmultiqc
- Alignment using
STAR
- Quantification using
rsem
orfeatureCounts
- TCR analysis using
TraCeR
. - BCR analysis using
BraCeR
.
nf-core/smartseq was originally written by Sandro Carollo, Giorgos Fotakis and Gregor Sturm