Index of /public/dataset/HiFiViral/Dec_2021

 Name                             Last modified      Size  Description
 Parent Directory                                      -   
 README.txt                       2021-12-07 14:07  2.1K  
 surveillance_samples.summary.csv 2021-12-07 09:45  8.0K  
 samples.vcf.zip                  2021-10-05 13:33  250K  
 all_samples_coverage.png         2021-10-05 13:27  658K  
 samples.consensus.fasta.zip      2021-10-05 13:33  767K  
 samples.consensus_mapped.bam.zip 2021-10-05 13:33  819K  
 samples.coverage.png.zip         2021-10-05 13:33   30M  
 samples.mapped.bam.zip           2021-10-05 13:33  515M  
 samples.hifi_reads.fastq.zip     2021-10-05 13:33  604M  

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)