https://github.com/bigbio/pgdb
ProteomeGenomics Database Creation - Nextflow Pipeline
https://github.com/bigbio/pgdb
cosmic ensembl mass-spectrometry nextflow nf-core proteogenomics proteomics
Last synced: 5 months ago
JSON representation
ProteomeGenomics Database Creation - Nextflow Pipeline
- Host: GitHub
- URL: https://github.com/bigbio/pgdb
- Owner: bigbio
- License: mit
- Created: 2021-01-19T20:12:48.000Z (over 5 years ago)
- Default Branch: dev
- Last Pushed: 2022-06-22T14:07:57.000Z (almost 4 years ago)
- Last Synced: 2025-09-05T08:41:29.628Z (9 months ago)
- Topics: cosmic, ensembl, mass-spectrometry, nextflow, nf-core, proteogenomics, proteomics
- Language: Nextflow
- Homepage:
- Size: 2.9 MB
- Stars: 2
- Watchers: 6
- Forks: 11
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Citation: CITATIONS.md
Awesome Lists containing this project
README
#  
[](https://github.com/nf-core/pgdb/actions?query=workflow%3A%22nf-core+CI%22)
[](https://github.com/nf-core/pgdb/actions?query=workflow%3A%22nf-core+linting%22)
[](https://nf-co.re/pgdb/results)
[](https://doi.org/10.5281/zenodo.4722662)
[](https://www.nextflow.io/)
[](https://docs.conda.io/en/latest/)
[](https://www.docker.com/)
[](https://sylabs.io/docs/)
[](https://tower.nf/launch?pipeline=https://github.com/nf-core/pgdb)
[](https://nfcore.slack.com/channels/pgdb)
[](https://twitter.com/nf_core)
[](https://www.youtube.com/c/nf-core)
## Introduction
**nf-core/pgdb** is a bioinformatics pipeline to generate proteogenomics databases. pgdb allows users to create proteogenomics databases using EMSEMBL as the reference proteome database. Three different major databases can be attached to the final proteogenomics database:
- The reference proteome (ENSEMBL Reference proteome)
- Non canonical proteins: pseudo-genes, sORFs, lncRNA.
- Variants: COSMIC, cBioPortal, GENOMAD variants
The pipeline allows to estimate decoy proteins with different methods and attach them to the final proteogenomics database.
The pipeline is built using [Nextflow](https://www.nextflow.io), 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
1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
3. Download the pipeline and test it on a minimal dataset with a single command:
```console
nextflow run nf-core/pgdb -profile test,YOURPROFILE --outdir
```
Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
> - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
> - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
> - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
> - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
4. Start running your own analysis!
```bash
nextflow run nf-core/pgdb -profile --ncrna true --pseudogenes true --altorfs true
```
> This will create a proteogenomics database with the ENSEMBL reference proteome and non canonical proteins like pseudo genes, non coding rnas or alternative open reading frames.
See [usage docs](https://nf-co.re/pgdb/usage) for all of the available options when running the pipeline.
## Pipeline Summary
By default, the pipeline currently performs the following:
- Download protein databases from ENSEMBL
- Translate from Genomics Variant databases into ProteoGenomics Databases (`COSMIC`, `GNOMAD`)
- Add to a Reference proteomics database, non-coding RNAs + pseudogenes.
- Compute Decoy for a proteogenomics databases
## Documentation
The nf-core/pgdb pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/pgdb/usage) and [output](https://nf-co.re/pgdb/output).
## Credits
nf-core/pgdb was originally written by Husen M. Umer (EMBL-EBI) & Yasset Perez-Riverol (Karolinska Institute)
## Contributions and Support
If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
For further information or help, don't hesitate to get in touch on the [Slack `#pgdb` channel](https://nfcore.slack.com/channels/pgdb) (you can join with [this invite](https://nf-co.re/join/slack)).
## Citations
The pgdb pipeline should be cited using the following citation:
> Umer HM, Audain E, Zhu Y, Pfeuffer J, Sachsenberg T, Lehtiö J, Branca R, Perez-Riverol Y. Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides.
>
> _Bioinformatics_. 2021 Dec 14;38(5):1470–2. doi: [10.1093/bioinformatics/btab838](https://dx.doi.org/10.1093/bioinformatics/btab838). Epub ahead of print. PMID: 34904638; PMCID: PMC8825679.
additionally you can cite the pipeline directly with the following doi: 10.5281/zenodo.4722662
An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
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](https://dx.doi.org/10.1038/s41587-020-0439-x).