# sanger-tol/genomenote: Citations

## [sanger-tol/genomenote](https://pipelines.tol.sanger.ac.uk/genomenote)

## [nf-core](https://nf-co.re)

> 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](https://www.nextflow.io)

> 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](https://github.com/NBISweden/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](https://bedtools.readthedocs.io/en/latest/)

  > 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](https://busco.ezlab.org)

  > 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](https://cooler.readthedocs.io/en/latest/)

  > 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](https://github.com/jkbonfield/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](https://github.com/thegenemyers/FASTK)

- [GeneScopeFK](https://github.com/thegenemyers/GENESCOPE.FK)

- [GFastats](https://github.com/vgl-hub/gfastats)

  > Giulio Formenti, Linelle Abueg, Angelo Brajuka, Nadolina Brajuka, Cristóbal Gallardo-Alba, Alice Giani, Olivier Fedrigo, Erich D Jarvis, Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs, Bioinformatics, Volume 38, Issue 17, September 2022, Pages 4214–4216, https://doi.org/10.1093/bioinformatics/btac460

- [GFFREAD](https://github.com/gpertea/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](https://github.com/thegenemyers/MERQURY.FK)

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

  > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

- [NCBI Datasets CLI](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/)

- [R](https://www.r-project.org)

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

- [Samtools](https://www.htslib.org)

  > 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](https://conda.org/)

  > 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](https://bioconda.github.io)

  > 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](https://biocontainers.pro)

  > 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](https://www.docker.com)

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

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > 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.