At the Centre for Research in Infectious Diseases (CRID), we are committed to advancing scientific discovery by providing high-quality genomics and bioinformatics services. Our team combines deep expertise with cutting-edge technologies to support researchers across a wide range of disciplines. We offer comprehensive next-generation sequencing (NGS) and data analysis services, tailored to meet the needs of academic, clinical, and industry partners. With access to a broad portfolio of platforms and chemistries, we guide our collaborators in selecting the most effective solutions to achieve their research goals.

A) Quality Control

Sample quality is critical to the success of any sequencing project. At CRID’s Genomics Hub, we use state-of-the-art equipment to assess the integrity and purity of all DNA and RNA samples before sequencing. This ensures high-quality data and minimizes the risk of sample failure.

Our QC platforms include:

• Agilent TapeStation 4150 – for fragment analysis and sizing
• Qubit Fluorometers – for accurate quantification of nucleic acids
• NanoDrop Spectrophotometer – for purity assessment
• Gel Electrophoresis Systems – for visualizing DNA/RNA integrity
   

B) Short-Read Sequencing

Illumina’s sequencing-by-synthesis technology is the global standard for short-read sequencing. At CRID, we operate both the NovaSeq 6000 and MiSeq platforms, offering scalable solutions for projects of all sizes.

Short-read sequencing is ideal for applications such as:

• Infectious disease research
• Cancer genomics
• Agrigenomics
• Environmental studies
• Human and microbial transcriptomics
• Food safety and metagenomics
• Animal and plant microbiome studies

1. NovaSeq 6000

High-throughput sequencing for large-scale projects

The NovaSeq 6000 delivers exceptional speed, scalability, and cost-efficiency for high-volume sequencing. It supports a wide range of applications, including:

• Whole-genome and exome sequencing
• Transcriptomics and epigenomics
• Targeted and amplicon sequencing
• Metagenomics and population-scale studies

2. MiSeq

Flexible, benchtop sequencing for targeted applications

The MiSeq is ideal for smaller-scale or targeted projects requiring fast turnaround and high accuracy. It supports:

• Amplicon and small genome sequencing
• Argeted resequencing
• Whole transcriptome analysis
• DNA methylation profiling
• Microbial community analysis

Case Study: The MiSeq platform was used at CRID to characterize microbial populations in mosquitoes, revealing links to insecticide resistance.
Read the study: https://doi.org/10.1186/s12866-025-04114-0
 

C) Long-Read Sequencing

Oxford Nanopore Technologies (ONT) offers real-time, long-read sequencing using nanopore-based detection. CRID provides access to both the MinION 1kB and PromethION platforms, enabling researchers to explore complex genomic regions and structural variants with high accuracy.

1. MinION 1kB

Portable, real-time sequencing for rapid insights

The MinION 1kB is a compact, field-ready device ideal for small-scale or time-sensitive projects. It supports:

• De novo genome assembly of plants, animals, and microbes
• Structural variation analysis in complex genomic regions
• Epigenetics, including direct detection of DNA methylation
• Pathogen surveillance and outbreak response (e.g., Ebola, Zika, COVID-19)

Additional Applications of Long-Read Sequencing

Metagenomics & Environmental Genomics:

• Long reads enhance species and strain-level resolution in complex microbial communities.
• Ideal for studying microbiomes, environmental DNA (eDNA), and antimicrobial resistance.

Transcriptomics:

• MinION 1kB platform supports full-length RNA sequencing, allowing researchers to study isoforms, alternative splicing, and RNA modifications.

Agrigenomics:

• De novo assembly of plant/animal genomes

Clinical & Diagnostic Research:

• Being explored for rapid point-of-care diagnostics, especially in infectious diseases such as malaria and cancer genomics.

2. PromethION Platform

Ultra-high-throughput, long-read sequencing for population-scale and complex genomics

The PromethION from Oxford Nanopore Technologies delivers real-time, long-read sequencing at scale. It uses nanopore-based detection to sequence DNA or RNA directly, offering:

• Ultra-long reads that span repetitive and complex genomic regions
• High accuracy in genome assembly and structural variant detection

Applications include:

• De novo genome assembly
• Structural variant and repeat region identification
• Full-length transcriptomics and alternative splicing analysis
• Epigenetic profiling
• Metagenomics

D) Sanger Sequencing & Fragment Analysis

High-accuracy DNA analysis for research and clinical applications

CRID offers trusted Sanger sequencing and fragment analysis services using advanced capillary electrophoresis technology. Our experienced team ensures fast turnaround and reliable, publication-ready results.

1. Sanger Sequencing

Gold-standard sequencing for targeted applications

Sanger sequencing remains the benchmark for:

• Mutation validation
• Cloning confirmation
• Targeted sequencing of specific genes or regions

We support a wide range of sample types, including animal, plant, insect, environmental, food, fungal, bacterial, viral, and parasitic DNA.

Our platform delivers:

• Read lengths up to 1000 bp
• Accuracy >99.99%
• Fast turnaround (within 7 working days)

Platform: ABI 3500xL Genetic Analyzer (24-capillary system)

Applications include:

• Mutation detection and verification
• Plasmid or construct confirmation
• PCR product sequencing
• CRISPR screening validation
• SNP genotyping

2. Fragment Analysis

High-resolution genotyping and fragment sizing

Our fragment analysis service supports:

• Microsatellite (SSR) genotyping
• STR profiling (e.g., forensics, cell line authentication)
• Loss of heterozygosity (LOH) analysis
• SNP detection via SNaPshot
• Mutation detection (e.g., fragment length polymorphism)
• CRISPR screening (indel analysis)

Using the ABI 3500xL, we offer:

• Accurate sizing from 50 bp to >1000 bp
• Multiplexing capabilities
• Optional expert data interpretation and troubleshooting

E) Data Analysis

Custom bioinformatics support tailored to your project

Our bioinformatics team—comprising PhD-level scientists and postdocs—offers expert analysis of NGS datasets across all platforms. We design bespoke pipelines to meet the specific needs of each project.

Common services include:

• Short-read mapping and SNP detection
• Metabarcoding analysis (alpha/beta diversity, differential abundance)
• Shotgun metagenomics (taxonomic and functional profiling)
• RNA-seq differential expression and splicing analysis
• Small RNA and epigenetic data analysis
• De novo genome and transcriptome assembly and annotation
• Structural variant and methylation profiling