sheylle1/vircapseq-respiratory-surveillance

Code and de-identified metadata supporting the analyses in the VirCapSeq-VERT respiratory virus surveillance study in South Africa. # Implementation of VirCapSeq-VERT Metagenomic Surveillance for Respiratory Viruses in South Africa This repository contains the code and de-identified metadata used for the analyses presented in the manuscript: > **Implementation of hybridisation capture metagenomic surveillance for respiratory viruses in South Africa** ## Overview This study evaluates the implementation of the VirCapSeq-VERT hybridisation capture metagenomic sequencing assay for respiratory virus surveillance in South Africa.The repository supports reproducible research. *Note*: Materials in this repository may be updated upon final publication. ## Repository Contents ``` scripts/ Analysis scripts data/ De-identified sample metadata results/ Generated figures and summary tables ``` ## Data Availability Human-read-removed FASTQ files are publicly available from the NCBI Sequence Read Archive (SRA): **BioProject:** PRJNA1455986 Consensus genome sequences have been submitted to GISAID (accession numbers provided in Supplementary Table X). Only de-identified metadata required to reproduce the analyses is included in this repository. ## Reproducing the Analysis 1. Download the human-read-removed FASTQ files from the SRA. 2. Obtain the consensus genome sequences from GISAID (where permitted). 3. Clone this repository. 4. Install the required software and dependencies. 5. Run the analysis scripts in the order indicated in the `scripts/` directory. ## Software Analyses were performed using: * R (version 4.3.3) * Python (version 3) * Genome Detective (v2.17–2.21) * Nextclade (v3.21.0) * FastQC (v0.11.2) * MultiQC Additional package versions are provided in the individual analysis scripts. ## Contact For questions or issues regarding this repository, please contact the corresponding author listed in the manuscript.