id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-346145-hnfeauow	Pillay, Sureshnee	Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic	2020-08-17		.txt	text/plain	7281	371	56	title: Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic In our SARS-CoV-2 assembly workflow, the initial assembly obtained from Genome Detective was polished by aligning mapped reads to the reference (NC_045512) and filtering out mutations with low genotype likelihoods, using bcftools 1.7-2 mpileup method. Furthermore, reagents for only 24 samples were available, as the order of Illumina TruSeq DNA Library preparation kit (x 96 sample libraries), which was placed in February and was enough to produce 480 genomes, had not arrived, due to the restrictions on international flights. The Nextera Flex library preparation kit was suggested by their technical team as a potentially better and quicker solution to produce SARS-CoV-2 genomes, which we found to be true. The Nextera Flex DNA library preparation kit was also evaluated, and we found it saved up to nine hours of hands-on time, when compared with the original ARTIC protocol that uses TruSeq. All three library preparation methods produced high-quality genomes.	./cache/cord-346145-hnfeauow.txt	./txt/cord-346145-hnfeauow.txt