A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
nf-core/epitopeprediction is a bioinformatics best-practice analysis pipeline for epitope prediction and annotation. The pipeline performs epitope predictions for a given set of variants or peptides directly using state of the art prediction tools. Additionally, resulting prediction results can be annotated with metadata.
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.
Download the pipeline and test it on a minimal dataset with a single command:
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.
Start running your own analysis!
See usage docs for all of the available options when running the pipeline.
The nf-core/epitopeprediction pipeline comes with documentation about the pipeline which you can read at https://nf-co.re/epitopeprediction.
nf-core/epitopeprediction was originally written by Christopher Mohr from Institute for Translational Bioinformatics and Quantitative Biology Center and Alexander Peltzer from Böhringer Ingelheim. Further contributions were made by Sabrina Krakau from Quantitative Biology Center.
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
If you use nf-core/epitopeprediction for your analysis, please cite it using the following doi: 10.5281/zenodo.3564666
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.