OVERVIEW
SEQUENCING CORE FACILITY
The Sequencing Core Facility was established in January 2016. The facility operates several next-generation sequencers and maintains a fully equipped laboratory and staff able to perform a variety of sequencing applications. Services performed include sample preparation and data generation, followed by the delivery of partially analysed sequence information back to NICD centres and collaborators.
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, established in January 2016, aims to enhance research and surveillance efforts at the NICD by offering precise, high-quality, and cost-effective next-generation sequencing (NGS) solutions. Currently, it serves all NICD centers, extending their NGS and bioinformatics capabilities.
Since its inception, the core facility has actively participated in numerous projects spanning from conception to completion. Key areas of focus include whole genome sequencing (de novo and re-sequencing), custom amplicon sequencing, viral and bacterial metagenomics, and human exome sequencing.
Equipped with three Illumina Nextseq 2000 sequencers, one Nextseq 1000 sequencer, and a Pacbio Sequel, the facility also features a dedicated genomics server for data analysis. This server boasts 8 nodes, 288 cores, 2.5TB RAM, and 0.5PB storage, with an additional 0.5PB on a Lenovo backup server. Further enhancements to the High-Performance Computing (HPC) infrastructure are underway, including a 120TB NAS storage device and 2 GPUs with 512GB RAM and 2 x 960GB NVMe SSDs.
The 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 neighbor-joining tree generation.
Additionally, NF-Core delivers a suite of standardized and reproducible Nextflow pipelines for diverse bioinformatics analyses such as genomics, transcriptomics, and proteomics. Furthermore, access to automated Illumina Dragen pipelines—including Amplicon, Enrichment, Germline, RNA, and Single Cell RNA workflows—is available.
LEADERSHIP AND TEAM
SEQUENCING CORE FACILITY
Dr Arshad Ismail is the head of the NICD Sequencing Core Facility. Prior to moving to NICD, Dr Ismail spent seven years at a private biotechnology company, Inqaba Biotec (PTY) Ltd as the Next- generation sequencing (NGS) Manager.
Through his tenure at Inqaba Biotec he established various NGS applications across different platforms, providing specific solutions in the NGS business environment. Since 2014, he has been employed at NICD as a Medical Scientist heading the Sequencing Core Facility. In this position he has played a vital role in developing NGS solutions for research and surveillance activities at the NICD. These include TB and HIV drug resistance surveillance, HIV antibody research, vaccine epitope identification, molecular epidemiology, viral zoonosis studies and outbreak response
Administrator
Johanna Msalela
Tel: +27 11 555 0450
Email: johannam@nicd.ac.za
Bioinformatics Scientist
Dr Mushal Ali
Email: mushala@nicd.ac.za
Bioinformatics Scientist
Dr Stanford Kwenda
Email: stanfordk@nicd.ac.za
Medical Scientist
Dr Zamantungwa Khumalo
Email: zamantungwak@nicd.ac.za
Medical Scientist
Dr Senzo Mtshali
Email: senzom@nicd.ac.za
Medical Technologist
Florah Mnyameni
Email: florahm@nicd.ac.za
SEQUENCING REQUEST
To facilitate sequencing requests and streamline the process, we’ve introduced a dedicated section on our website where users can submit their sequencing requests directly to our center. The request form includes essential details such as name, institution, contact information, and sample specifications.
Users can specify sample names, types, genome sizes, desired sequencing coverage, and provide descriptions for each sample. Additionally, the form includes guidelines for sample quality control and handling after sequencing. This ensures that submitted samples meet our recommended input requirements for successful sequencing outcomes. We aim to provide a seamless experience for researchers seeking sequencing services at our facility, with clear instructions to guide them through the submission process.
