NGS-SA: Genomic and Bioinformatic protocols to SARS-CoV-2

NGS-SA are committed to open science and sharing all protocols to capacitate laboratories in Africa and abroad.
As part of a grant from the SAMRC and the DSI, we have already set up five laboratories in South Africa.
If you are a laboratory and want to learn about our protocols, please contact NGS-SA.

GENOMIC PROTOCOLS FOR SARS-COV-2

We have implemented open protocols for Ilumina, Oxford Nanopore Technologies and S5 Ion DNA sequencers. We have also developed two new protocols that use NEB and Nextera Flex for library preparation in Illumina. These protocols save six to nine hours of hands on time, which is important to laboratories in South Africa that lack automation. In order to allow other laboratories in the world to learn from our experience, we have made all of our protocols freely available and are training other laboratories in South Africa and abroad.

Genomic protocols

The protocols are available at Protocols.io and on our website.

Bioinformatics protocols

We produced a bioinformatics protocol on Genome Detective for all of the main sequencing platforms. pre-print publication is also available here.

Download Protocols

NEBnext library construction and sequencing for SARS-CoV-2: Adapting COVID-19 ARTIC...

2020-07-26

Giandhari J, Pillay S, Tegally H, Wilkinson E, Chimukangara B, Lessells R, Moosa Y, Gazy I, Fish M, Singh L, Khanyile KS, Fonseca V, Giovanetti M, Alcantara LC, de Oliveira T

COVID-19 Analysis on Galaxy

2020-07-07

Quadram Institute, SANBI, University of Melbourne, BC Centre for Disease Control

SARS-COV-2 genome assembly using Genome Detective

2020-06-20

Koen Deforche, Houriiyah Tegally and Tulio De Oliveira

SARS-COV-2 sequencing using Illumina Nextera DNA Flex Library

2020-06-15

Jennifer Giandhari and Sureshnee Pillay

SARS-COV-2 sequencing using Illumina NEB Next Library

2020-06-14

Jennifer Giandhari and Sureshnee Pillay

SARS-CoV-2 Sequencing Resources: US CDC resources

2020-05-07

US Center for Disease Control (US CDC)

VIDEO ON SEQUENCING SARS-COV-2 TO CONTROL OUTBREAKS IN SOUTH AFRICA

This is a short video that provides information on KRISP, which is one of the genomics facilities of the NGS-SA. In this video, we describe how sequencing was produced in South Africa to control a large nosocomial outbreak. The video also describe the NGS-SA consortium and how we work with the Africa CDC to expand genomics use on the continent.

Watch other videos on our work here