nf-core/slamseq is a bioinformatics analysis pipeline used for SLAMSeq sequencing data.
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.
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
singularityand 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.
The nf-core/slamseq pipeline comes with documentation about the pipeline, found in the
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
If you would like to contribute to this pipeline, please see the contributing guidelines.
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.
An extensive list of references for the tools used by the pipeline can be found in the