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neoantigen-pipeline

Pipeline for computing neoantigen qualities from DNA and RNA-Seq data

https://github.com/mskcc/neoantigen-pipeline

Science Score: 57.0%

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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 16 DOI reference(s) in README
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    Low similarity (10.8%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Pipeline for computing neoantigen qualities from DNA and RNA-Seq data

Basic Info
  • Host: GitHub
  • Owner: mskcc
  • License: mit
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 9.75 MB
Statistics
  • Stars: 2
  • Watchers: 6
  • Forks: 0
  • Open Issues: 12
  • Releases: 6
Created about 2 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

mskcc/neoantigenpipeline

GitHub Actions CI Status GitHub Actions Linting StatusCite with Zenodo nf-test

Nextflow run with conda run with docker run with singularity Launch on Seqera Platform

Introduction

mskcc/neoantigenpipeline is a bioinformatics pipeline that adapts Luksza et al.'s neoantigenEditing and fitness pipeline for usage by investigators in MSK. The pipeline curently supports working with TEMPO output mafs, Facets gene-level copy number calls, and Polysolver outputs. It outputs a json representation of the clonal structure of the tumor annotated with neoantigen burden, driver burden, and fitness of the clone. Also individual neoantigens are labeled with the quality of the neoantigen as described by Luksza et al.

Workflow Diagram

  1. Create phylogenetic trees using PhyloWGS
  2. Use netMHCpan-4 to calculate binding affinities
  3. Use netMHCpanStab to calculate stability scores
  4. Use Luksza et al.'s neoantigen quality and fitness computations tool (NeoantigenEditing) to evaluate peptides

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv:

csv sample,maf,facets_hisens_cncf,hla_file tumor_normal,temp_test_somatic_unfiltered.maf,facets_hisens.cncf.txt,winners.hla.txt tumor_normal2,temp_test_somatic_unfiltered.maf,facets_hisens.cncf.txt,winners.hla.txt

Now, you can run the pipeline using:

bash nextflow run mskcc/neoantigenpipeline \ -profile prod,<docker/singularity> \ --input samplesheet.csv \ --outdir <OUTDIR>

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

  • Deshwar, A. G., Vembu, S., Yung, C. K., Jang, G. H., Stein, L., & Morris, Q. (2015). PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome biology, 16(1), 35. https://doi.org/10.1186/s13059-015-0602-8
  • Jurtz, V., Paul, S., Andreatta, M., Marcatili, P., Peters, B., & Nielsen, M. (2017). NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data. Journal of immunology (Baltimore, Md. : 1950), 199(9), 3360–3368. https://doi.org/10.4049/jimmunol.1700893
  • Łuksza, M., Sethna, Z.M., Rojas, L.A. et al. Neoantigen quality predicts immunoediting in survivors of pancreatic cancer. Nature 606, 389–395 (2022). https://doi.org/10.1038/s41586-022-04735-9
  • Rasmussen, M., Fenoy, E., Harndahl, M., Kristensen, A. B., Nielsen, I. K., Nielsen, M., & Buus, S. (2016). Pan-Specific Prediction of Peptide-MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity. Journal of immunology (Baltimore, Md. : 1950), 197(4), 1517–1524. https://doi.org/10.4049/jimmunol.1600582

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

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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.

Owner

  • Name: Memorial Sloan Kettering
  • Login: mskcc
  • Kind: organization
  • Email: perinj@mskcc.org
  • Location: New York, NY, USA

Citation (CITATIONS.md) 

# mskcc/neoantigenpipeline: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [Phylowgs](https://github.com/morrislab/phylowgs)

  > Deshwar, A. G., Vembu, S., Yung, C. K., Jang, G. H., Stein, L., & Morris, Q. (2015). PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome biology, 16(1), 35. https://doi.org/10.1186/s13059-015-0602-8

- [NetMHCPan-4](https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/)

  > Jurtz, V., Paul, S., Andreatta, M., Marcatili, P., Peters, B., & Nielsen, M. (2017). NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data. Journal of immunology (Baltimore, Md. : 1950), 199(9), 3360–3368. https://doi.org/10.4049/jimmunol.1700893

- [NeoantigenEditing](https://github.com/LukszaLab/NeoantigenEditing)

  > Łuksza, M., Sethna, Z.M., Rojas, L.A. et al. Neoantigen quality predicts immunoediting in survivors of pancreatic cancer. Nature 606, 389–395 (2022). https://doi.org/10.1038/s41586-022-04735-9

- [NetMHCPanStab](https://services.healthtech.dtu.dk/services/NetMHCstabpan-1.0/)
  > Rasmussen, M., Fenoy, E., Harndahl, M., Kristensen, A. B., Nielsen, I. K., Nielsen, M., & Buus, S. (2016). Pan-Specific Prediction of Peptide-MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity. Journal of immunology (Baltimore, Md. : 1950), 197(4), 1517–1524. https://doi.org/10.4049/jimmunol.1600582

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

GitHub Events

Total
  • Create event: 18
  • Issues event: 4
  • Release event: 5
  • Watch event: 2
  • Delete event: 10
  • Issue comment event: 17
  • Push event: 55
  • Pull request review event: 14
  • Pull request event: 35
Last Year
  • Create event: 18
  • Issues event: 4
  • Release event: 5
  • Watch event: 2
  • Delete event: 10
  • Issue comment event: 17
  • Push event: 55
  • Pull request review event: 14
  • Pull request event: 35

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 180
  • Total Committers: 3
  • Avg Commits per committer: 60.0
  • Development Distribution Score (DDS): 0.183
Past Year
  • Commits: 180
  • Committers: 3
  • Avg Commits per committer: 60.0
  • Development Distribution Score (DDS): 0.183
Top Committers
Name Email Commits
Nikhil Kumar n****6@g****m 147
John Orgera 6****h 32
John Orgera o****j@m****g 1
Committer Domains (Top 20 + Academic)
mskcc.org: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 4
  • Total pull requests: 19
  • Average time to close issues: N/A
  • Average time to close pull requests: 10 days
  • Total issue authors: 2
  • Total pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.95
  • Merged pull requests: 15
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 18
  • Average time to close issues: N/A
  • Average time to close pull requests: 6 days
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.94
  • Merged pull requests: 14
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nikhil (34)
  • johnoooh (3)
Pull Request Authors
  • nikhil (32)
  • johnoooh (10)
Top Labels
Issue Labels
enhancement (4) bug (1)
Pull Request Labels

Dependencies

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modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
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