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nf-core/taxprofiler: Citations

Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. In Nature Biotechnology (Vol. 38, Issue 3). https://doi.org/10.1038/s41587-020-0439-x

Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. In Nature Biotechnology (Vol. 35, Issue 4). https://doi.org/10.1038/nbt.3820

Pipeline tools

Software packaging/containerisation tools

  • Anaconda

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

  • Bioconda

    Dale, R., Grüning, B., Sjödin, A., Rowe, J., Chapman, B. A., Tomkins-Tinch, C. H., Valieris, R., Batut, B., Caprez, A., Cokelaer, T., Yusuf, D., Beauchamp, K. A., Brinda, K., Wollmann, T., Corguillé, G. Le, Ryan, D., Bretaudeau, A., Hoogstrate, Y., Pedersen, B. S., … Köster, J. (2018). Bioconda: Sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7). https://doi.org/10.1038/s41592-018-0046-7

  • BioContainers

    Da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: An open-source and community-driven framework for software standardization. Bioinformatics, 33(16). https://doi.org/10.1093/bioinformatics/btx192

  • 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, G. M., Sochat, V., & Bauer, M. W. (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE, 12(5). https://doi.org/10.1371/journal.pone.0177459

Data

  • Maixner (2021) (CI Test Data)

    Maixner, F., Sarhan, M. S., Huang, K. D., Tett, A., Schoenafinger, A., Zingale, S., Blanco-Míguez, A., Manghi, P., Cemper-Kiesslich, J., Rosendahl, W., Kusebauch, U., Morrone, S. R., Hoopmann, M. R., Rota-Stabelli, O., Rattei, T., Moritz, R. L., Oeggl, K., Segata, N., Zink, A., … Kowarik, K. (2021). Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period. Current Biology, 31(23). https://doi.org/10.1016/j.cub.2021.09.031

  • Meslier (2022) (AWS Full Test data)

    Meslier, V., Quinquis, B., Da Silva, K., Plaza Oñate, F., Pons, N., Roume, H., Podar, M., & Almeida, M. (2022). Benchmarking second and third-generation sequencing platforms for microbial metagenomics. Scientific Data, 9(1). https://doi.org/10.1038/s41597-022-01762-z