nf-core pipeline · archived ·
nf-core/smartseq2
A Nextflow pipeline for preprocessing single-cell RNA-seq data generated with the Smart-seq2 protocol.
What nf-core/smartseq2 is
nf-core/smartseq2 is a bioinformatics pipeline designed to process single-cell RNA sequencing data produced using the Smart-Seq2 protocol. Originally written by Sandro Carollo, Giorgos Fotakis and Gregor Sturm, it executes tasks using the Nextflow workflow manager to ensure portability across computational infrastructures.
The pipeline handles primary data processing from raw sequence reads to quality metrics, genomic alignment, and expression quantification. It also integrates specialised tools for recovering adaptive immune receptor sequences from single cells. The pipeline is archived and no longer maintained.
What the pipeline does
The workflow begins by performing read quality control on sequencing inputs using FastQC, with summary visualisations aggregated by MultiQC. Reads are aligned against a reference genome using STAR, after which gene expression quantification is conducted using either RSEM or featureCounts.
For immunological studies, the pipeline can additionally reconstruct full-length paired T-cell receptor sequences using TraCeR and B-cell receptor sequences using BraCeR directly from the single-cell transcriptomic reads.
Key facts
- Pipeline engine
- Nextflow
- Assay type
- Smart-Seq2 single-cell RNA-seq
- Input format
- FASTQ (.fastq.gz)
- Alignment software
- STAR
- Quantification tools
- RSEM, featureCounts
- Immune profiling
- TraCeR (TCR), BraCeR (BCR)
- Quality control
- FastQC, MultiQC
- Status
- Archived (no longer maintained)
What you can use it for
- Smart-Seq2 transcript quantification
- Align single-cell RNA reads to a reference genome with STAR and generate expression estimates using RSEM or featureCounts.
- T-cell receptor reconstruction
- Reconstruct and analyse single-cell T-cell receptor sequences using TraCeR.
- B-cell receptor reconstruction
- Assemble and profile single-cell B-cell receptor repertoires using BraCeR.
- Single-cell library quality control
- Evaluate sequencing quality across multiple single-cell libraries using FastQC and MultiQC.
Strengths and limits
Good at
- Integrates both T-cell and B-cell receptor reconstruction alongside standard transcriptomic quantification.
- Provides flexibility between RSEM and featureCounts for expression quantification.
- Uses Docker or Singularity containerisation to ensure reproducibility across compute systems.
Watch out for
- The project is archived and receives no further updates or maintenance.
- Configured specifically for Smart-Seq2 protocol data rather than droplet-based single-cell platforms.
Questions
Can I run nf-core/smartseq2 without my own cluster?
The research agent runs nf-core/smartseq2 with Nextflow on its own machine — up to 32 cores, 256 GiB of memory and 24 hours per run, which covers the test profile and real single-sample runs. It builds the samplesheet, checks it against the pipeline's schema and reads the results back. When a run is too big for one machine, it gives you the exact command for your own cluster instead.
What licence is nf-core/smartseq2 under?
MIT, like every nf-core pipeline.
What tools are available for gene and transcript quantification?
The pipeline can quantify expression levels using either RSEM or featureCounts after alignment with STAR.
Does this pipeline support immune receptor assembly?
Yes, it incorporates TraCeR for T-cell receptor analysis and BraCeR for B-cell receptor analysis.
Is the pipeline actively maintained?
No, the pipeline repository is archived and is no longer maintained.
How to cite it
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.
Written from nf-core/smartseq2's own README. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.