OVERVIEW                                                                                                                                                                                                                                                                         
    Human extracts sequenced with the HiFiViral SARS-CoV-2 kit from PacBio
    These data are provided as an example of typical performance in surveillance samples at 96-plex
    Samples sequenced by University of Georgia Genomics and Bioinformatics Core

PROTOCOL
    https://www.pacb.com/wp-content/uploads/Procedure-Checklist-%E2%80%93-PacBio-HiFiViral-High-Throughput-Multiplexing-for-Full-Viral-Genome-Sequencing-of-SARS-CoV-2.pdf

SMRTLINK DOCUMENTATION
    https://www.pacb.com/wp-content/uploads/SMRT_Link_User_Guide_v10.2.pdf
    
METHODS
    Samples         	Human extracts sequenced for surveillance by the University of Georia Genomics and Bioinformatics Core
    RNA extraction	TBD
    Experimental Design 96 samples including two positive controls (Twist 14 and 17) and 2 negative non-template controls
    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

DATA FILES
    samples.hifi_reads.fastq.zip		Processed HiFi reads: demultiplexed, trimmed, and QCed (96 samples)
    samples.mapped.bam.zip			Processed HiFi reads mapped to Wuhan reference NC.045512.2 (96 samples)
    samples.consensus.fasta.zip			Consensus sequences (96 samples)
    samples.consensus_mapped.bam.zip		Consensus sequences (split at interior Ns) and mapped to Wuhan reference NC.045512.2 (96 samples)    
    samples.vcf.zip				Variant calls relative to Wuhan reference NC.045512.2 (96 samples)
    surveillance_samples.summary.csv		Table of results by samplem includes sample Ct
    all_samples_coverage.png			Summary of coverage across all samples
    samples.coverage.png.zip			Coverage plot for each sample (96 samples)