nf-core/slamseq

Edit

Introduction

nf-core/slamseq is a bioinformatics analysis pipeline used for SLAMSeq sequencing data.

The workflow processes SLAMSeq datasets using Slamdunk and infers direct transcriptional targets using DESeq2.

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/slamseq -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/slamseq -profile <docker/singularity/conda/institute> --input design.tsv --genome GRCh38

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

Documentation

The nf-core/slamseq 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

Credits

nf-core/slamseq was originally written by Tobias Neumann (@t-neumann) for the use at the IMP Vienna.

Many thanks to other who have helped out along the way too, including (but not limited to): @apeltzer, @drpatelh, @pditommaso, @maxulysse, @ewels, @zethson, @bgruening, @micans.

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

If you use nf-core/slamseq for your analysis, please cite it using the following doi: 10.5281/zenodo.3826585

You can cite slamdunk as follows:

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets.

Tobias Neumann, Veronika A. Herzog, Matthias Muhar, Arndt von Haeseler, Johannes Zuber, Stefan L. Ameres & Philipp Rescheneder.

BMC Bioinformatics 2019 May 20. doi: 10.1186/s12859-019-2849-7.

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

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.