id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-333420-qqyg9um9	Zhu, Xun	idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates	2020-10-09		.txt	text/plain	460	35	58	title: idCOV: a pipeline for quick clade identification of SARS-CoV-2 isolates idCOV is a phylogenetic pipeline for quickly identifying the clades of SARS-CoV-2 virus isolates from raw sequencing data based on a selected clade-defining marker list. Using a public dataset, we show that idCOV can make equivalent calls as annotated by Nextstrain.org on all three common clade systems using user uploaded FastQ files directly. The on-going Coronavirus disease 2019 (Covid-19) pandemic has resulted in over 734,000 deaths, affect-20 ing more than 188 countries and territories (CSSE, 2020; Dong, et al., 2020) . Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; previously known as 2019-nCoV) 23 is the pathogenic cause of Covid-19 (Lescure, et al., 2020) . In order to quickly identify the clade of an isolate of SARS-Cov-2 given its sequencing FastQ files, 30 we have developed a bioinformatics pipeline and a user-friendly web interface.	./cache/cord-333420-qqyg9um9.txt	./txt/cord-333420-qqyg9um9.txt