SARS-CoV-2 Raw Sequencing Data from IDRL, AKU, Pakistan

This project aims to provide guidelines/SoPs to laboratories and relevant stakeholders in making decisions on establishing sequencing capacities and capabilities in Low-and-Middle Income Countries (LMICs). We Align/Harmonize the already and newly collected case report forms (CRFs)/contextual/metadata, using Go Data developed by the Global Outbreak Alert and Response Network (GOARN), Member States and partners, of selected samples for sequencing according to PHA4GE SoPs/contextual data specification. Sequencing was performed by following the SARS-CoV-2 ARCTIC v3 protocol. After the generation of sequencing data, we implemented The Chan Zuckerberg BioHub and Chan Zuckerberg Initiative Bioinformatics workflow, that is, ARTIC protocol-specific Workflow Description Language (WDL)-supported IDSeq pipeline for building SARS-CoV-2 variant calling and consensus genomes. We are submit raw SARS-CoV-2 FASTQ data to the databases of the International Nucleotide Sequence Database Collaboration (INSDC), e.g., SRA. We already submitted consensus/assembled SARS-CoV-2 data to the GISAID database.The objectives of this project are:Objective 1: Data analysis of in-process sequencing samples by implementing and managing open source, interoperable reproducible Bioinformatics data analysis pipeline to our existing Bioinformatics infrastructure.Objective 2: Report the findings of SARS-CoV-2 genomic characterizations, that is, variants of interest (VOIs) and variants of concerns (VOCs) by publicly sharing the consensus genomes assemblies.