Index of /public/dataset/HiFiViral/Jan_2022
Name Last modified Size Description
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Parent Directory -
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README.txt 2022-01-05 12:52 3.3K
InqabaOmicronSamples.csv 2022-01-04 15:52 5.6K
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m64187e_211217_130958.hifi_reads.bam 2022-01-03 11:18 1.6G
InqabaOmicronSamples_PlateQC.csv 2022-01-03 11:15 2.0K
InqabaOmicronSamples_Barcoded_Sample.csv 2022-01-03 11:13 1.5K
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samples.hifi_reads.fastq.zip 2021-12-20 06:51 426M
samples.mapped.bam.zip 2021-12-20 06:46 326M
sample_summary.csv 2021-12-20 06:46 3.6K
samples.consensus.fasta.zip 2021-12-20 06:46 299K
samples.consensus_mapped.bam.zip 2021-12-20 06:46 328K
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all_samples_coverage.png 2021-12-20 06:46 675K
samples.vcf.zip 2021-12-20 06:46 116K
samples.raw.vcf.zip 2021-12-20 06:46 132K
samples.coverage.png.zip 2021-12-20 06:46 12M
HiFiViral_Barcoded_M13_Primer_Plate.fasta 2021-11-01 19:31 1.9K
OVERVIEW
Data collected by Inqaba Biotec using HiFiViral SARS-CoV-2
Run of 39 samples suspected of being Omicron plus 3 Delta variant samples
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 25 Human swabs stored in Bosphore liquid collection media
RNA isolation Three methods used:
All samples (25) were collected using Bosphore liquid collection media
https://www.launchdiagnostics.com/product-list/bosphore-ex-tract-dry-swab-rna-solution/
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
https://www.zymoresearch.com/collections/rna-clean-concentrator-kits-rcc
Batch C: Viral RNA was extracted from Bosphore media using Zymo Quick-Viral RNA kit before RT PCR, cDNA amplification and barcoding
https://www.zymoresearch.com/collections/quick-rna-viral-kits
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
m64187e_211217_130958.hifi_reads.bam HiFi reads (unprocessed)
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)
samples.raw.vcf.zip 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
samples.coverage.png.zip Coverage plot for each sample (96 samples)
InqabaOmicronSamples.csv Table of results plus sample info (Ct, clade assignment, RNA extraction method, etc)
SMRTLINK FILES
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)
PROBE AND BARCODE FILES
HiFiViral_Barcoded_M13_Primer_Plate.fasta Barcoded M13 Primer Sequences