CITATIONS.md

Arcadia-Science/seqqc: Citations

nf-core

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. (2020). The nf-core framework for community-curated bioinformatics pipelines. https://doi.org/10.1038/s41587-020-0439-x

Nextflow

Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. (2017). Nextflow enables reproducible computational workflows. https://doi.org/10.1038/nbt.3820

Pipeline tools

• FastQC

• MultiQC

  Ewels P, Magnusson M, Lundin S, Käller M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. https://doi.org/10.1093/bioinformatics/btw354

• Sourmash

  Brown CT, Irber L. (2016). Sourmash: a library for MinHash sketching of DNA. https://doi.org/10.21105/joss.00027

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. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. https://doi.org/10.1038/s41592-018-0046-7

• 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. (2017). BioContainers: an open-source and community-driven framework for software standardization. https://doi.org/10.1093/bioinformatics/btx192

• Docker

• Singularity

  Kurtzer GM, Sochat V, Bauer MW. (2017). Singularity: Scientific containers for mobility of compute. https://doi.org/10.1371/journal.pone.0177459