
@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 = { M�lder, F and Jablonski, KP and Letcher, B and Hall, MB and Tomkins-Tinch, CH and Sochat, V and Forster, J and Lee, S and Twardziok, SO and Kanitz, A and Wilm, A and Holtgrewe, M and Rahmann, S and Nahnsen, S and K�ster, J},
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}
}