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sanger-tol/ascc: 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

  • FCS-adaptor

    Astashyn, Alexander, Eric S. Tvedte, Deacon Sweeney, Victor Sapojnikov, Nathan Bouk, Victor Joukov, Eyal Mozes, et al. 2023. “FCS-Adaptor.” FCS-Adaptor. June 6, 2023. ———. 2024. “Rapid and Sensitive Detection of Genome Contamination at Scale with FCS-GX.” Genome Biology 25 (1): 60.

  • Kcounter.

    Buchfink, Benjamin, Klaus Reuter, and Hajk-Georg Drost. 2021. “Sensitive Protein Alignments at Tree-of-Life Scale Using DIAMOND.” Nature Methods 18 (4): 366–68. Camargo, Antônio. 2020. “Kcounter.” Kcounter. February 17, 2020. https://github.com/apcamargo/kcounter.

  • BlobToolKit.

    Challis, Richard, Edward Richards, Jeena Rajan, Guy Cochrane, and Mark Blaxter. 2020. “BlobToolKit - Interactive Quality Assessment of Genome Assemblies.” G3 10 (4): 1361–74. Diaz, Alexander Ramos, Zaynab Butt, Priyanka Surana, Richard Challis, Sujai Kumar, and Matthieu Muffato. 2023. “BlobToolKit Pipeline.” BlobToolKit Pipeline. May 18, 2023.

  • Tiara.

    Karlicki, Michał, Stanisław Antonowicz, and Anna Karnkowska. 2022. “Tiara: Deep Learning-Based Classification System for Eukaryotic Sequences.” Bioinformatics 38 (2): 344–50.

  • Minimap2.

    Li, Heng. 2018. “Minimap2: Pairwise Alignment for Nucleotide Sequences.” Bioinformatics 34 (18): 3094–3100.

  • TensorFlow

    Martín Abadi, Ashish Agarwal, Paul Barham, Eugene Brevdo, Zhifeng Chen, Craig Citro, Greg S. Corrado, et al. 2015. “TensorFlow: Large-Scale Machine Learning on Heterogeneous Systems.”

  • VecScreen.

    NCBI. 2001. “NCBI VecScreen.” NCBI VecScreen. October 5, 2001.

  • [Scikit-Learn] Pedregosa, F., G. Varoquaux, A. Gramfort, and V. Michel. 2011. “Scikit-Learn: Machine Learning in Python. JMLR 12, 2825–2830 (2011).” Journal of Machine Learning Research 12 (October): 2825–30.

Software packaging/containerisation tools

  • Conda

    conda contributors. conda: A system-level, binary package and environment manager running on all major operating systems and platforms. Computer software. https://github.com/conda/conda

  • 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.