paper.bib

@article{otoole_pango_2022,
	title = {Pango lineage designation and assignment using {SARS}-{CoV}-2 spike gene nucleotide sequences},
	volume = {23},
	issn = {1471-2164},
	url = {https://doi.org/10.1186/s12864-022-08358-2},
	doi = {10.1186/s12864-022-08358-2},
	abstract = {More than 2 million SARS-CoV-2 genome sequences have been generated and shared since the start of the COVID-19 pandemic and constitute a vital information source that informs outbreak control, disease surveillance, and public health policy. The Pango dynamic nomenclature is a popular system for classifying and naming genetically-distinct lineages of SARS-CoV-2, including variants of concern, and is based on the analysis of complete or near-complete virus genomes. However, for several reasons, nucleotide sequences may be generated that cover only the spike gene of SARS-CoV-2. It is therefore important to understand how much information about Pango lineage status is contained in spike-only nucleotide sequences. Here we explore how Pango lineages might be reliably designated and assigned to spike-only nucleotide sequences. We survey the genetic diversity of such sequences, and investigate the information they contain about Pango lineage status.},
	number = {1},
	journal = {BMC Genomics},
	author = {O’Toole, Áine and Pybus, Oliver G. and Abram, Michael E. and Kelly, Elizabeth J. and Rambaut, Andrew},
	month = feb,
	year = {2022},
	pages = {121},
}

@article{roach_ten_2022,
	title = {Ten simple rules and a template for creating workflows-as-applications},
	volume = {18},
	issn = {1553-7358},
	url = {https://dx.plos.org/10.1371/journal.pcbi.1010705},
	doi = {10.1371/journal.pcbi.1010705},
	language = {en},
	number = {12},
	urldate = {2024-10-02},
	journal = {PLOS Computational Biology},
	author = {Roach, Michael J. and Pierce-Ward, N. Tessa and Suchecki, Radoslaw and Mallawaarachchi, Vijini and Papudeshi, Bhavya and Handley, Scott A. and Brown, C. Titus and Watson-Haigh, Nathan S. and Edwards, Robert A.},
	editor = {Markel, Scott},
	month = dec,
	year = {2022},
	pages = {e1010705},
	file = {PDF:/Users/wwirth/Zotero/storage/FAQ4GMUT/Roach et al. - 2022 - Ten simple rules and a template for creating workflows-as-applications.pdf:application/pdf},
}
@Article{10.12688/f1000research.29032.2,
AUTHOR = {Mölder, Felix and Jablonski, Kim PHilipp and Letcher, Brice and Hall, Michael B. and Tomkins-Tinch, Christopher H, and Sochat, Vanessa and Forster, Jan and Lee, Soohyun and Twardziok, Sven O. and Kanitz, Alexander and Wilm, Andreas and Holtgrewe, Manuel and Rahmann, Sven and Nahnsen, Sven and Köster, Johannes},
TITLE = {Sustainable data analysis with Snakemake [version 2; peer review: 2 approved]
},
JOURNAL = {F1000Research},
VOLUME = {10},
YEAR = {2021},
NUMBER = {33},
DOI = {10.12688/f1000research.29032.2}
}