Supply and Deliver of Next Generation Sequencing Bioinformatics Software (5Years)
Tender Details
- Tender Title: Supply and Deliver of Next Generation Sequencing Bioinformatics Software for a Period of Five (5) Years at Human Genetics Department, Universitas Bloemfontein
- Tender Number: RFQ No. 671096
- Tender Status: Open RFQ
- Advert Date: 16 September 2026
- Closing Date: 29 September 2026
- Closing Time: 11:00 AM
- Required At: National Health Laboratory Service (NHLS)
- Department: Human Genetics Department, Universitas, Bloemfontein
- Location: Bloemfontein, Free State
- Tender Category: Computer Software Supply and License Management; Information and Communications Technology
- Briefing Session: N/A
- Contact for Queries: Neo Mokgosi
- Required Documents: As listed in the RFQ documentation and marked mandatory
Tender Description
The National Health Laboratory Service (NHLS) invites quotations for the supply and delivery of Next Generation Sequencing (NGS) bioinformatics software for a five-year period at the Human Genetics Department at Universitas, Bloemfontein.
The solution is intended to support genomic data analysis, clinical variant interpretation and modernise the department’s bioinformatics capabilities. The software must support clinical diagnostic workflows while meeting specified data privacy and regulatory requirements.
Scope of Work
The successful supplier will be responsible for:
- Supplying and delivering the NGS bioinformatics software solution.
- Providing a five-year software subscription.
- Installing and deploying the software.
- Providing local desktop deployment with local server extension capabilities.
- Providing comprehensive operator training.
- Supplying detailed software documentation.
- Providing ongoing technical support throughout the five-year contract.
- Providing software upgrades at no additional cost during the contract period.
- Updating variant classification algorithms in line with evolving clinical guidelines.
- Supporting integration with existing laboratory workflows.
- Ensuring the solution meets applicable clinical, regulatory and data-security requirements.
Technical Requirements
The required software solution must include:
Licensing
- Annual subscription-based licensing.
- Token-based licensing is not permitted.
- Pay-per-sample licensing structures are excluded.
- Pricing must remain fixed in South African Rand, excluding VAT, as specified in the tender requirements.
Clinical and Regulatory Compliance
- Registered CE-IVD certification for clinical diagnostic use.
- Compliance with at least one recognised data protection framework:
- HIPAA
- GDPR
- POPIA
NGS and Microarray Data Formats
The software must support standard genomic data formats, including:
- FAST5
- FASTQ
- BAM
- CRAM
- GVCF
- VCF
- BED
- TSV
Variant Analysis and Interpretation
The platform must provide an automated interpretation pipeline capable of analysing:
- Single nucleotide variants (SNVs)
- Insertions and deletions (Indels)
- Copy number variants (CNVs)
- Structural variants (SVs)
Germline variant classification must adhere to recognised ACMG or ACGS guidelines.
Database and Data Management
The solution must provide:
- Local database storage.
- Integrated data visualisation.
- Quality-control reporting.
- Comprehensive audit trails.
- Automatic alerts when ClinVar variants are reclassified.
- Predefined annotation sources.
- A customisable variant knowledge database.
- Literature referencing functionality.
Clinical Reporting
The software must support clinical report generation in:
- DOCX format
- PDF format
Upgrades and Technical Support
The successful supplier must provide written commitments confirming that:
- Software upgrades will be provided at no additional cost throughout the five-year contract.
- Variant classification algorithm updates will be provided as clinical guidelines evolve.
- Ongoing technical support will be available throughout the contract period.
Skills and Supplier Requirements
Although the tender does not prescribe specific personnel qualifications, suppliers should demonstrate proven expertise in:
- Clinical bioinformatics software deployment.
- Genomic data pipeline management.
- Clinical diagnostic software implementation.
- Regulatory compliance.
- Local server configuration.
- User training and technical support.
- Laboratory information system integration.
- Clinical genetics workflows.
- ACMG/ACGS variant interpretation standards.
- Healthcare data security and patient-data protection.
Previous experience supplying similar diagnostic software to public health or academic institutions is advantageous.
Key Technical and Regulatory Terms
CE-IVD: A European conformity marking associated with in vitro diagnostic medical devices and indicating conformity with applicable EU requirements for diagnostic use.
ACMG/ACGS: Guidelines used by clinical laboratories to classify genetic variants according to their potential clinical significance.
ClinVar: A database containing information about relationships between human genetic variants and their clinical significance. The required software must alert users when relevant variant classifications are reclassified.
POPIA, HIPAA and GDPR: Data protection frameworks governing the handling and protection of personal or sensitive information in South Africa, the United States and the European Union respectively.
Annual Subscription License: A recurring licensing model required for the software, rather than token-based or usage-based billing.
Tender Evaluation and Pricing
The tender summary indicates that evaluation will follow an 80/20 preference point system, with price competitiveness and specified B-BBEE goals forming part of the evaluation.
Pricing must be fixed in South African Rand, excluding VAT, and cover the applicable delivery, installation, supervision and overhead costs specified in the tender requirements.