NGS-SA: Open science and sharing data rapidly but believe that research should be fair

NGS-SA are committed to open science and sharing all data as rapidly as possible but believe that research should be fair.
Please note that the data shared is the work of hundreds of people and must be treated as unpublished data.
If you wish to analyse the data and publish research, pleasee contact NGS-SA to ensure that those who have generated the data can be involved.

ALL DATA IS MADE PUBLIC AND IT IS CURATED BY AN TEAM OF AFRICAN SCIENTISTS AT GISAID

We have entered in a partnership with GISAID so all of our genomic data is publicly available at databases as soon as it is produced. We truly believe in fair research practices and in the need to capacitate local researchers and health care workers. We also believe that all of those involved in sampling, producing, annotating and analysing the data need to be properly acknowledged. We are working with other African networks to also train bioinformaticians so data can be also analysed quickly and accurately in Africa.

Public Data

All of our data is public but we request that you treat it as unpublished and contact us if you want to analyze and publish from it.

Data Curation & Analysis

We have also partnered with H3Africa H3AbioNet so scientists from many African countries can participate in this activity.

Download Data

GISAID

2021-11-21

Sequences: Updated regularly > 23,500

Dataset include assembled whole Genomes from South Africa (i.e. > 90% coverage, < 10% NNNs)

Short Read Archive (SRA) at NCBI

2021-11-06

Sequences: Updated regularly > 10,000

FASTQ files from NGS-SA. These were generated in Illumina and Oxford Nanopore Technologies (ONT)

GISAID

2021-10-07

Sequences: Updated regularly > 20,000

Dataset include assembled whole Genomes from South Africa (i.e. > 90% coverage, < 10% NNNs)

Short Read Archive (SRA) at NCBI

2021-10-06

Sequences: Updated regularly > 9000

FASTQ files from NGS-SA. These were generated in Illumina and Oxford Nanopore Technologies (ONT)

GISAID

2021-09-06

Sequences: Updated regularly > 17,500

Dataset include assembled whole Genomes from South Africa (i.e. > 90% coverage, < 10% NNNs)

GISAID

2021-07-02

Sequences: Updated regularly > 10,500

Dataset include assembled whole Genomes from South Africa (i.e. > 90% coverage, < 10% NNNs)

GISAID

2021-06-12

Sequences: Updated regularly > 8400

Dataset include assembled whole Genomes from South Africa (i.e. > 90% coverage, < 10% NNNs)

Short Read Archive (SRA) at NCBI

2021-06-11

Sequences: Updated regularly > 7000

FASTQ files from NGS-SA. These were generated in Illumina and Oxford Nanopore Technologies (ONT)

GISAID

2021-03-03

Sequences: > 3900

Dataset include > 1,000 genomes from the new Spike Variant 501Y.V2 (B.1.351, 20H) - Whole Genomes from South Africa...

Short Read Archive (SRA)

2021-02-04

Sequences: Updated regularly > 4000

501Y.V2 (B.1.351) FASTQ files from NGS-SA. These were generated in Illumina and Oxford Nanopore Technologies (ONT)

GISAID

2021-02-04

Sequences: > 3150

Dataset include > 400 genomes from the new Spike Variant 501Y.V2 - Whole Genomes from South Africa (i.e. > 90%...

GISAID

2020-12-19

Sequences: > 2700

Dataset include > 200 genomes from the new Spike Variant 501Y.V2 - Whole Genomes from South Africa (i.e. > 90%...

GISAID

2020-11-15

Sequences: > 2000

Whole Genomes from South Africa (i.e. > 90% coverage, < 10% NNNs)

GISAID

2020-10-29

Sequences: > 1700

Whole Genomes from South Africa (i.e. > 90% coverage, < 10% NNNs)

GISAID

2020-09-15

Sequences: > 1400

Whole Genomes from South Africa (i.e. > 90% coverage, < 10% NNNs)

GISAID

2020-08-28

Sequences: > 1000

Whole Genomes from South Africa (i.e. > 90% coverage, < 10% NNNs)

GISAID

2020-08-13

Sequences: > 800

Whole Genomes from South Africa (i.e. > 90% coverage, < 10% NNNs)

GISAID

2020-08-05

Sequences: > 600

Whole Genomes from South Africa (i.e. > 90% coverage, < 10% NNNs)

Short Read Archive (SRA)

2020-08-05

Sequences: Updated regularly > 500

FASTQ Illumina and SRA files from KRISP at UKZN.

GISAID

2020-07-23

Sequences: > 400

SARS-CoV-2 whole Genome sequences from South Africa (i.e. > 90% coverage, < 10% NNNs)

GISAID

2020-07-17

Sequences: > 350

SARS-CoV-2 whole Genome sequences from South Africa (i.e. > 90% coverage, < 10% NNNs)

GISAID

2020-07-14

Sequences: > 300

Whole Genomes from South Africa (i.e. > 90% coverage, < 10% NNNs)

Short Read Archive (SRA)

2020-07-05

Sequences: Updated regularly > 300

FASTQ Illumina and SRA files from KRISP at UKZN.

GISAID

2020-07-05

Sequences: > 220

Whole Genomes from South Africa (i.e. > 90% coverage, < 10% NNNs)

GISAID

2020-06-16

Sequences: Update regularly > 170

Whole Genomes from South Africa (i.e. > 90% coverage, < 10% NNNs)

Short Read Archive (SRA)

2020-06-16

Sequences: Updated regularly > 100

FASTQ Illumina and SRA files from KRISP at UKZN.

GISAID

2020-04-15

Sequences: 21

Early strains from KwaZulu-Natal

HIGH QUALITY DATA PRODUCED WITH GENOME DETECTIVE

Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately. We have fine-tuned Genome Detective to assembly high quality genomes of SARS-CoV-2. Our software is very easy to use allowing our laboratory scientists to assemble genomes as soon as they come out of the DNA sequencers.

Step by step protocol

Easy to use protocol and videos to help African researchers to assembly high-quality genomes.

Training program

Training African scientists and curators to quickly assemble genomes from Illumina, Nanopore and S5 Ion platforms.

Access the publication and protocols for assembly of data

VIDEO ON Curation and Analysis of Data in Africa by Africans

Short video about genomic data curation, analysis and bioinformatics software development in South Africa. The Network for Genomics Surveillance is an ambitious project to challenge the status quo and allow high level scientific knowledge to be implemented in Africa to help to understand and control viruses outbreaks, such as COVID-19.

Visit our Youtube Channel