# nf-core/epitopeprediction: 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

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

- [SnpSift](https://dx.doi.org/10.3389/fgene.2012.00035)

  > Pablo Cingolani, Viral M. Patel, Melissa Coon, Tung Nguyen, Susan J. Land, Douglas M. Ruden and Xiangyi Lu. Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift. _Frontiers in Genetics_ 3, 35 (2012). doi: 10.3389/fgene.2012.00035.

- [Epytope (FRED2)](https://dx.doi.org/10.1093/bioinformatics/btw113)

  > Benjamin Schubert, Mathias Walzer, Hans-Philipp Brachvogel, András Szolek, Christopher Mohr, Oliver Kohlbacher. FRED 2: an immunoinformatics framework for Pythonö Bioinformatics 32(13), 2044-2046 (2016). doi: 10.1093/bioinformatics/btw113.

- [MHCflurry](https://dx.doi.org/10.1016/j.cels.2018.05.014)

  > Timothy J. O’Donnell, Alex Rubinsteyn, Maria Bonsack, Angelika B. Riemer, Uri Laserson, Jeff Hammerbacher. MHC flurry: open-source class I MHC binding affinity prediction. Cell systems 7(1), 129-132 (2018). doi: 10.1016/j.cels.2018.05.014.

- [MHCnuggets](https://dx.doi.org/10.1158/2326-6066.CIR-19-0464)

  > Xiaoshan M. Shao, Rohit Bhattacharya, Justin Huang, I.K. Ashok Sivakumar, Collin Tokheim, Lily Zheng, Dylan Hirsch, Benjamin Kaminow, Ashton Omdahl, Maria Bonsack, Angelika B. Riemer, Victor E. Velculescu, Valsamo Anagnostou, Kymberleigh A. Pagel and Rachel Karchin. High-throughput prediction of MHC class i and ii neoantigens with MHCnuggets. Cancer Immunology Research 8(3), 396-408 (2020). doi: 10.1158/2326-6066.CIR-19-0464.

- [NetMHC-4.0](https://pubmed.ncbi.nlm.nih.gov/26515819/)

  > Andreatta M, Nielsen M. Gapped sequence alignment using artificial neural networks: application to the MHC class I system. Bioinformatics. 2016 Feb 15;32(4):511-7. doi: 10.1093/bioinformatics/btv639. Epub 2015 Oct 29. PMID: 26515819; PMCID: PMC6402319.

- [NetMHCpan-4.0](https://pubmed.ncbi.nlm.nih.gov/28978689/)

  > Jurtz V, Paul S, Andreatta M, Marcatili P, Peters B, Nielsen M. NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data. J Immunol. 2017 Nov 1;199(9):3360-3368. doi: 10.4049/jimmunol.1700893. Epub 2017 Oct 4. PMID: 28978689; PMCID: PMC5679736.

- [NetMHCpan-4.1](https://pubmed.ncbi.nlm.nih.gov/32406916/)

  > Reynisson B, Alvarez B, Paul S, Peters B, Nielsen M. NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res. 2020 Jul 2;48(W1):W449-W454. doi: 10.1093/nar/gkaa379. PMID: 32406916; PMCID: PMC7319546.

- [NetMHCII-2.3](https://pubmed.ncbi.nlm.nih.gov/29315598/)

  > Jensen KK, Andreatta M, Marcatili P, Buus S, Greenbaum JA, Yan Z, Sette A, Peters B, Nielsen M. Improved methods for predicting peptide binding affinity to MHC class II molecules. Immunology. 2018 Jul;154(3):394-406. doi: 10.1111/imm.12889. Epub 2018 Feb 6. PMID: 29315598; PMCID: PMC6002223.

- [NetMHCII-2.3](https://pubmed.ncbi.nlm.nih.gov/29315598/)

  > Jensen KK, Andreatta M, Marcatili P, Buus S, Greenbaum JA, Yan Z, Sette A, Peters B, Nielsen M. Improved methods for predicting peptide binding affinity to MHC class II molecules. Immunology. 2018 Jul;154(3):394-406. doi: 10.1111/imm.12889. Epub 2018 Feb 6. PMID: 29315598; PMCID: PMC6002223.

- [NetMHCIIpan-4.0](https://pubmed.ncbi.nlm.nih.gov/32406916/)
  > Reynisson B, Alvarez B, Paul S, Peters B, Nielsen M. NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res. 2020 Jul 2;48(W1):W449-W454. doi: 10.1093/nar/gkaa379. PMID: 32406916; PMCID: PMC7319546.

## 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)

- [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.
