Index of /public/dataset/HiFiViral/Nov_2021
Name Last modified Size Description
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Parent Directory -
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samples.vcf.zip 2021-11-26 13:36 206K
samples.mapped.bam.zip 2021-11-26 13:36 589M
samples.hifi_reads.fastq.zip 2021-11-26 13:35 722M
samples.coverage.png.zip 2021-11-26 13:35 33M
samples.consensus_mapped.bam.zip 2021-11-26 13:35 785K
samples.consensus.fasta.zip 2021-11-26 13:35 702K
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sample_summary.csv 2021-11-26 13:36 7.9K
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m64012_210821_095651.hifi_reads.bam 2021-11-26 09:28 1.3G
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all_samples_coverage.png 2021-11-26 13:37 741K
README.txt 2021-11-29 16:25 2.8K
HiFiViral_SARS-CoV-2_TwistControls.PlateQC.csv 2021-11-26 09:54 4.5K
HiFiViral_SARS-CoV-2_TwistControls.Barcoded_Samples.csv 2021-11-28 16:21 3.9K
HiFiViral_Barcoded_M13_Primer_Plate.fasta 2021-11-01 19:31 1.9K
OVERVIEW
Example data for HiFiViral SARS-CoV-2 for Synthetic RNA Controls
These control sequences are NOT FULL LENGTH and consist of non-overlapping 5kb fragments
Controls were diluted to the following copy numbers: 6E6, 3E6, 1E6, 1E5, 1E4, 1E3, 100, 25
Samples with >= 10,000 copies have > 95% genome coverage
Samples with >= 1000 copies have > 90% genome coverage
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 Twist Bioscience control RNAs: 14 (Alpha), 15 (Alpha), 16 (Beta), 17 (Gamma)
Experimental Design 4 Controls X 8 input quantities X 3 replicates = 96 samples
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
m64012_210821_095651.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)
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)
SMRTLINK FILES
HiFiViral_SARS-CoV-2_TwistControls.PlateQC.csv Input file specifying barcode IDs, sample name, plate ID, and well coordinate (required for SMRTlink plateQC report)
HiFiViral_SARS-CoV-2_TwistControls.Barcoded_Samples.csv Input file specifying barcode IDs and sample names (required for Demultiplex Barcodes)
PROBE AND BARCODE FILES
HiFiViral_SARS-CoV-2_Enrichment_Probes.fasta Probe Arm Sequences
HiFiViral_Barcoded_M13_Primer_Plate.fasta Barcoded M13 Primer Sequences
KNOWN ISSUES
Multi-strain detection for samples with Ct >= 26 is not supported, false positives may be observed