CITATIONS.md

sanger-tol/genomenote: Citations

sanger-tol/genomenote

nf-core

Ewels, Philip A., et al. “The Nf-Core Framework for Community-Curated Bioinformatics Pipelines.” Nature Biotechnology, vol. 38, no. 3, Feb. 2020, pp. 276–78, https://doi.org/10.1038/s41587-020-0439-x.

Nextflow

Di Tommaso, Paolo, et al. “Nextflow Enables Reproducible Computational Workflows.” Nature Biotechnology, vol. 35, no. 4, Apr. 2017, pp. 316–19, https://doi.org/10.1038/nbt.3820.

Pipeline tools

• AGAT

  Dainat J. AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF/GFF format. (Version v1.4.0). Zenodo. https://www.doi.org/10.5281/zenodo.3552717

• BedTools

  Quinlan, Aaron R., and Ira M. Hall. “BEDTools: A Flexible Suite of Utilities for Comparing Genomic Features.” Bioinformatics, vol. 26, no. 6, 2010, pp. 841–842., https://doi.org/10.1093/bioinformatics/btq033.

• BUSCO

  Manni, Mosè, et al. “BUSCO: Assessing Genomic Data Quality and Beyond.” Current Protocols, vol. 1, no. 12, Dec. 2021, https://doi.org/10.1002/cpz1.323.

• Cooler

  Abdennur, Nezar, and Leonid A Mirny. “Cooler: Scalable Storage for Hi-C Data and Other Genomically Labeled Arrays.” Bioinformatics, vol. 36, no. 1, 2019, pp. 311–316., https://doi.org/10.1093/bioinformatics/btz540.

• Crumble

  James K Bonfield, Shane A McCarthy, and Richard Durbin. "Crumble: reference free lossy compression of sequence quality values" Bioinformatics, Volume 35, Issue 2, January 2019, Pages 337–339, https://doi.org/10.1093/bioinformatics/bty608

• FastK

• GFFREAD

  Pertea G and Pertea M. "GFF Utilities: GffRead and GffCompare [version 1; peer review: 3 approved]". F1000Research 2020, 9:304 https://doi.org/10.12688/f1000research.23297.1

• MerquryFK

• MultiQC

  Ewels, Philip, et al. “MultiQC: Summarize Analysis Results for Multiple Tools and Samples in a Single Report.” Bioinformatics, vol. 32, no. 19, 2016, pp. 3047–3048., https://doi.org/10.1093/bioinformatics/btw354.

• NCBI Datasets CLI

• R

  R Core Team. “R: A Language and Environment for Statistical Computing.” 4.2.0, R Foundation for Statistical Computing, 2020.

• Samtools

  Danecek, Petr, et al. “Twelve Years of SAMtools and BCFtools.” GigaScience, vol. 10, no. 2, Jan. 2021, https://doi.org/10.1093/gigascience/giab008.

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, Björn, et al. “Bioconda: sustainable and comprehensive software distribution for the life sciences.", Nature Methods, vol. 15, Jul. 2018, pp. 475-6, https://doi.org/10.1038/s41592-018-0046-7.

• BioContainers

  da Veiga, Felipe, et al. “BioContainers: an open-source and community-driven framework for software standardization.", Bioinformatics, vol. 33, no. 16, Aug. 2017, pp. 2580-2, https://doi.org/10.1093/bioinformatics/btx192.

• Docker

  Merkel, Dirk, et al. “Docker: Lightweight Linux Containers for Consistent Development and Deployment.", Association for Computing Machinery, vol. 2014, no. 239, Mar. 2014.

• Singularity

  Kurtzer, Gregory M., et al. “Singularity: Scientific containers for mobility of compute.", PLOS ONE, vol. 12, no. 5, May 2017, pp. e0177459, https://doi.org/10.1371/journal.pone.0177459.