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nf-core/reportho: Citations

nf-core

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

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

  • OMA

Adrian M Altenhoff, Clément-Marie Train, Kimberly J Gilbert, Ishita Mediratta, Tarcisio Mendes de Farias, David Moi, Yannis Nevers, Hale-Seda Radoykova, Victor Rossier, Alex Warwick Vesztrocy, Natasha M Glover, Christophe Dessimoz, OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more, Nucleic Acids Research, Volume 49, Issue D1, 8 January 2021, Pages D373–D379, https://doi.org/10.1093/nar/gkaa1007

Thomas PD, Ebert D, Muruganujan A, Mushayahama T, Albou L-P, Mi H. PANTHER: Making genome-scale phylogenetics accessible to all. Protein Science. 2022; 31: 8–22. https://doi.org/10.1002/pro.4218

Yannis Nevers, Arnaud Kress, Audrey Defosset, Raymond Ripp, Benjamin Linard, Julie D Thompson, Olivier Poch, Odile Lecompte, OrthoInspector 3.0: open portal for comparative genomics, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D411–D418, https://doi.org/10.1093/nar/gky1068

Jaime Huerta-Cepas, Damian Szklarczyk, Davide Heller, Ana Hernández-Plaza, Sofia K Forslund, Helen Cook, Daniel R Mende, Ivica Letunic, Thomas Rattei, Lars J Jensen, Christian von Mering, Peer Bork, eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D309–D314, https://doi.org/10.1093/nar/gky1085

The UniProt Consortium , UniProt: the Universal Protein Knowledgebase in 2023, Nucleic Acids Research, Volume 51, Issue D1, 6 January 2023, Pages D523–D531, https://doi.org/10.1093/nar/gkac1052

Huang H, McGarvey PB, Suzek BE, Mazumder R, Zhang J, Chen Y, Wu CH. A comprehensive protein-centric ID mapping service for molecular data integration. Bioinformatics. 2011 Apr 15;27(8):1190-1. doi: 10.1093/bioinformatics/btr101. PMID: 21478197; PMCID: PMC3072559.

Jumper, J., Evans, R., Pritzel, A. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021). https://doi.org/10.1038/s41586-021-03819-2

Mihaly Varadi, Stephen Anyango, Mandar Deshpande, Sreenath Nair, Cindy Natassia, Galabina Yordanova, David Yuan, Oana Stroe, Gemma Wood, Agata Laydon, Augustin Žídek, Tim Green, Kathryn Tunyasuvunakool, Stig Petersen, John Jumper, Ellen Clancy, Richard Green, Ankur Vora, Mira Lutfi, Michael Figurnov, Andrew Cowie, Nicole Hobbs, Pushmeet Kohli, Gerard Kleywegt, Ewan Birney, Demis Hassabis, Sameer Velankar, AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D439–D444, https://doi.org/10.1093/nar/gkab1061

Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000 Sep 8;302(1):205-17. doi: 10.1006/jmbi.2000.4042. PMID: 10964570.

B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler, R. Lanfear (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., 37:1530-1534. https://doi.org/10.1093/molbev/msaa015

D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, L.S. Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35:518–522. https://doi.org/10.1093/molbev/msx281

Vincent Lefort, Richard Desper, Olivier Gascuel, FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program, Molecular Biology and Evolution, Volume 32, Issue 10, October 2015, Pages 2798–2800, https://doi.org/10.1093/molbev/msv150

Software packaging/containerisation tools

  • Anaconda

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

  • Bioconda

    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

    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

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

  • Singularity

    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.