OVERVIEW
SEQUENCING CORE FACILITY
Established in January 2016, the NICD Sequencing Core Facility is a specialised, ISO 17025-accredited unit providing next-generation sequencing (NGS) services in support of public health surveillance, research, and outbreak response. The facility is equipped with advanced sequencing platforms, including the Illumina NovaSeq X Plus, and is staffed by a skilled team of scientists and technical personnel dedicated to delivering high-quality genomic data.
Core services include NGS library preparation, high-throughput sequencing, and the provision of quality-assured, partially analysed sequence data to NICD centres and collaborating institutions. The facility supports all NICD centres and plays a key role in national and international research collaborations.
Recent achievements include the successful sequencing of whole human genomes on the NovaSeq X Plus platform and the rapid sequencing of outbreak samples with turnaround times as short as three days. These accomplishments reflect the facility’s commitment to innovation, responsiveness, and scientific excellence in support of public health.
OBJECTIVES
SEQUENCING CORE FACILITY
- To provide NGS and Bioinformatics support for surveillance, research activities and outbreak response at the NICD.
- Expand into the area of core genome pathogens using NGS.
- Run and maintain a cost effective and a high quality innovative sequencing facility.
- Stimulate research and training in the both NGS and bioinformatics.
Functions
The NICD Sequencing Core Facility plays a pivotal role in advancing public health research, surveillance, and outbreak response by delivering precise, high-throughput, and cost-effective next-generation sequencing (NGS) services. Serving all NICD centres, the facility enhances both sequencing and bioinformatics capacities across a broad spectrum of applications and public health priorities.
Since its inception, the facility has contributed to numerous projects from initial planning through to data delivery. Core areas of expertise include whole genome sequencing (both de novo and re-sequencing), targeted amplicon sequencing, viral and bacterial metagenomics, and human exome sequencing.
The facility is equipped with a comprehensive suite of high-throughput sequencing and automation platforms, including:
- 1 Illumina NovaSeq X Plus
- 3 Illumina NextSeq 2000 sequencers
- 1 Illumina NextSeq 1000 sequencer
- 1 Element Biosciences AVITI system
- 1 PacBio Vega benchtop system
- 2 Hamilton NGS STAR liquid handling robots
These platforms are supported by a dedicated on-site genomics server for data processing and analysis. The high-performance computing (HPC) server boasts 9 nodes, 416 cores, 3TB RAM, and 0.5PB storage with one node containing 2× L40 NVIDIA GPUs combined with 128 CPUs and 500GB of RAM. Additional computing infrastructure includes a 120TB NAS storage device and an additional 0.5PB on a Lenovo backup server. The facility also houses an Illumina DRAGEN server, providing hardware-accelerated genomic analysis for rapid, accurate secondary analysis of NGS data.
The HPC genomics server provides secure, potent, and adaptable bioinformatic computing accessible to all NICD scientists. It hosts various pipelines, including the Jekesa pipeline, which focuses on Illumina paired-end WGS data for bacterial whole genome assembly and typing, offering virulence predictions and conducting reference-free alignments, SNP-site analysis, clustering, and neighbour-joining tree generation.
With this infrastructure, the facility has the potential to process thousands of libraries per month and generate multiple terabases of sequencing data weekly, depending on project needs. High-throughput automation, combined with rapid turnaround capabilities, allows for timely sequencing—such as processing outbreak-related samples within 72 hours—without compromising data quality.
LEADERSHIP AND TEAM
SEQUENCING CORE FACILITY
Prof Arshad Ismail is a distinguished figure in molecular biology and genomics, currently holding the position of Head of the NICD Sequencing Core Facility. His career has been marked by a steadfast commitment to advancing next-generation sequencing (NGS) technologies and their practical applications in public health.
Before joining NICD, Prof. Ismail served as the NGS Manager at Inqaba Biotec (PTY) Ltd, a prominent biotechnology firm, from 2007 to 2013. This seven-year tenure allowed him to refine his expertise in NGS methodologies, which proved instrumental in his later contributions to the field. Since his arrival at NICD in 2014 Prof. Ismail has been the driving force behind the establishment and expansion of the Sequencing Core Facility. This facility, now equipped with seven advanced NGS instruments, provides essential support to eight distinct centers within NICD, thereby facilitating critical research and surveillance efforts across a spectrum of infectious diseases.
Beyond his responsibilities at NICD, Prof. Ismail maintains affiliations with esteemed academic institutions, including the Durban University of Technology, the University of Venda, and the University of the Witwatersrand. These collaborations underscore his dedication to bridging the divide between academic research and practical application, thereby fostering innovation and the exchange of knowledge.
Laboratory Manager
Andrew Moultrie
Email: andrewm@nicd.ac.za
Bioinformatics Scientist
Dr Jonathan Featherston
Email: jonathanf@nicd.ac.za
Bioinformatics Scientist
Dr Mishalan Moodley
Email: mishalanm@nicd.ac.za
Senior Medical Scientist
Dr Senzo Mtshali
Email: senzom@nicd.ac.za
Medical Scientist
Thabo Mohale
Email: thabom@nicd.ac.za
Medical Technologist
Florah Mdhuli
Email: florahm@nicd.ac.za
SEQUENCING REQUEST
Researchers and collaborators seeking sequencing services from the NICD Sequencing Core Facility can download the sequencing request form here.
Completed forms should be submitted via email to: sequencinglab@nicd.ac.za
The form captures essential information such as the requester’s name, institution, contact details, and detailed sample specifications, including sample names, types, genome sizes, desired sequencing coverage, and relevant project notes. It also includes guidelines for sample quality control and handling, helping ensure submitted material meets the facility’s input standards.
The dashboard provides key metrics on turnaround times, instrument utilisation, and project volumes.
Below is a summary of our yearly sequencing output: