Index of /public/dataset/HiFiViral/Jan_2022

Icon  Name                                      Last modified      Size  Description
[PARENTDIR] Parent Directory - [   ] HiFiViral_Barcoded_M13_Primer_Plate.fasta 2021-11-01 19:31 1.9K [TXT] InqabaOmicronSamples.csv 2022-01-04 15:52 5.6K [TXT] InqabaOmicronSamples_Barcoded_Sample.csv 2022-01-03 11:13 1.5K [TXT] InqabaOmicronSamples_PlateQC.csv 2022-01-03 11:15 2.0K [TXT] README.txt 2022-01-05 12:52 3.3K [IMG] all_samples_coverage.png 2021-12-20 06:46 675K [   ] m64187e_211217_130958.hifi_reads.bam 2022-01-03 11:18 1.6G [TXT] sample_summary.csv 2021-12-20 06:46 3.6K [   ] 2021-12-20 06:46 299K [   ] 2021-12-20 06:46 328K [   ] 2021-12-20 06:46 12M [   ] 2021-12-20 06:51 426M [   ] 2021-12-20 06:46 326M [   ] 2021-12-20 06:46 132K [   ] 2021-12-20 06:46 116K
    Data collected by Inqaba Biotec using HiFiViral SARS-CoV-2
    Run of 39 samples suspected of being Omicron plus 3 Delta variant samples  


    Samples         	25 Human swabs stored in Bosphore liquid collection media
    RNA isolation		Three methods used:
		All samples (25) were collected using Bosphore liquid collection media
		Batch A: samples processed directly from the Bosphore media. Upon collection, samples were immediately vortexed and incubated at 95*C for 8 minutes to release the viral material
		Batch B: samples from the Bosphore media were cleaned with Zymo RNA Clean and Concentrator before RT PCR, cDNA amplification and barcoding
		Batch C: Viral RNA was extracted from Bosphore media using Zymo Quick-Viral RNA kit before RT PCR, cDNA amplification and barcoding
    Viral Enrichment	HiFiViral SARS-CoV-2 Kit
    Library prep    	SMRTbell® Express Template Prep Kit 2.0 + Enzyme Clean Up Kit 2.0
    Sequencing      	Sequel IIe System, Sequel II Binding Kit 2.1, Sequel II Sequencing Plate 2.0, 8hr movie with no pre-extension
    Software        	ICS v10.1, SMRT® Link v10.2

    m64187e_211217_130958.hifi_reads.bam		HiFi reads (unprocessed)		Processed HiFi reads: demultiplexed, trimmed, and QCed (96 samples)			Processed HiFi reads mapped to Wuhan reference NC.045512.2 (96 samples)			Consensus sequences (96 samples)		Consensus sequences (split at interior Ns) and mapped to Wuhan reference NC.045512.2 (96 samples)				Variant calls relative to Wuhan reference NC.045512.2 (96 samples)			Variant calls relative to Wuhan reference NC.045512.2 before filtering on allele frequency (96 samples)
    sample_summary.csv				Table of results by sample
    all_samples_coverage.png			Summary of coverage across all samples			Coverage plot for each sample (96 samples)
    InqabaOmicronSamples.csv			Table of results plus sample info (Ct, clade assignment, RNA extraction method, etc)

    InqabaOmicronSamples_PlateQC.csv		Input file specifying barcode IDs, sample name, plate ID, and well coordinate (required for SMRTlink plateQC report)
    InqabaOmicronSamples_Barcoded_Sample.csv	Input file specifying barcode IDs and sample names (required for Demultiplex Barcodes)

    HiFiViral_Barcoded_M13_Primer_Plate.fasta			Barcoded M13 Primer Sequences