Replication Data for: Enrichment approach for unbiased sequencing of respiratory syncytial virus directly from clinical samples

Version 3.0
Replication Data for: Enrichment approach for unbiased sequencing of respiratory syncytial virus directly from clinical samples
Waweru, Jacqueline W.; de Laurent, Zaydah; Kamau, Everlyn; Said, Khadija; Gicheru, Elijah; Mutunga, Martin; Kibet, Caleb; Kinyua, Johnson; Nokes, David James; Sande, Charles; Githinji, George, 2021, "Replication Data for: Enrichment approach for unbiased sequencing of respiratory syncytial virus directly from clinical samples", https://doi.org/10.7910/DVN/28LOAI, Harvard Dataverse, V3
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Description

This is a replication dataset for the manuscript titled: "Enrichment approach for unbiased sequencing of respiratory syncytial virus directly from clinical samples."

The data contains the results obtained after optimizing a metagenomics sequencing protocol for respiratory viruses with the main virus of interest being the respiratory syncytial virus (RSV); a leading cause of lower respiratory tract infections among children under the age of five. The Oxford Nanopore Technology MinION device was used for sequencig in this study. Besides, all the viral load results, nucleic acid concentrations obtained after performing real time PCR have also been included here.

Subject Medicine, Health and Life Sciences
Keyword metagenomics, sequencing, SISPA, RSV, centrifugal processing, Endoh primers, DNase, RNA
Notes Instruction for running analysis code

Data analysis R codes are numbered 1 to 3. The order ofR scripts is as follows:

  1. 1_boxplots_analysis: Contains codes used in generating all the box-plots generated from this data.
  2. 2_taxonomic_analysis:Contains codes that were used in analyzing the Kraken2 taxonomic classification reports.
  3. 3_MinION.sh: bash script containing the codes used in running Vsearch and primer matching using seqkit.
The R codes and datasets were generated using R version 3.6. In addition, Primers.fasta - A fasta file containing all the Endoh primers used in this study RSV_centroid.fasta - A fasta file containing the centroid sequence generated from the Illumina consensus sequences using Vsearch.

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JWaweru_Data_Codebook.pdf
JWaweru_Data_Codebook.pdf
Adobe PDF - 112.1 KB
Published Mar 17, 2021
8 Downloads
MD5: 578d0dd5a9502cd6e30ddfcb02a9fcbe
DocumentationVariable Codebook/Data Dictionary
Preview "JWaweru_Data_Codebook.pdf"
JWaweru_Data_Readme.txt
Plain Text - 6.3 KB
Published Mar 17, 2021
6 Downloads
MD5: cc2e952f8fbcd88d207da45f361623cc
DocumentationReadme
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data.zip
ZIP Archive - 762.6 KB
Published Mar 17, 2021
8 Downloads
MD5: f0a6131901b6f7fbecf1ba1d3b0550e1
Contains all data files used in the analysis
DataCSV and TXT
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1_boxplots_script.R
R Syntax - 7.1 KB
Published Mar 17, 2021
9 Downloads
MD5: 548b47ef87f4cfe927923d55585ceed3
Contains codes used in generating all the box-plots generated from this data
CodeR script (R version 3.6)
Preview "1_boxplots_script.R"
2_taxonomic_analysis.R
R Syntax - 12.3 KB
Published Mar 19, 2021
9 Downloads
MD5: 1edce1e147f8b9e15ce36c0a9817a46b
Contains codes that were used in analyzing the Kraken2 taxonomic classification reports
CodeR script (R version 3.6)
Preview "2_taxonomic_analysis.R"
3_MinION pipeline.sh
Shell Script - 2.8 KB
Published Mar 17, 2021
5 Downloads
MD5: e9fea7e673c32e4e87bcf956307dec30
bash script containing the codes used in running Vsearch and primer matching using seqkit
CodeExtended Data
bacterial_contamination_gel.jpg
bacterial_contamination_gel.jpg
JPEG Image - 802.2 KB
Published Apr 19, 2021
7 Downloads
MD5: 0a27189ab3f2ff9a01ab834529b6802e
Extended Data
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bacterial_contamination_reduction_gel.jpg
bacterial_contamination_reduction_gel.jpg
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Published Apr 19, 2021
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MD5: ce3309dd8eff63cfb2fc2480c40d08de
Extended Data
Preview "bacterial_contamination_reduction_gel.jpg"
primers.fasta
Unknown - 3.5 KB
Published Mar 17, 2021
7 Downloads
MD5: fffcff7885b9d2a6e6430b9832345004
A fasta file containing all the Endoh primers used in this study
Extended Data
RSV_centroid.fasta
Unknown - 45.4 KB
Published Mar 17, 2021
5 Downloads
MD5: b50918d9bbd87b26ebd578179e7f2de9
A fasta file containing the centroid sequence generated from the Illumina consensus sequences using Vsearch
Extended Data
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