Understand how your samples respond under different conditions. We quantify feature expression to reveal which genes are active, suppressed, or differentially expressed, giving you insights into biological pathways, disease mechanisms, and treatment effects.

Perfect for understanding cellular responses, validating targets, or exploring functional genomics.

Types of differential analysis:

Bulk RNA-seq:

Quantify and classify bulk RNA content by aligning overlapping short reads to the genome using STAR, and count reads aligned to known genes. Compare differential expression between treatment groups using edgeR, following robust statistical methods to deliver meaningful results and generate publication ready data. 

Related: Illumina Stranded mRNA, Illumina Total RNA, Small RNA

Single-cell RNA-seq: Single-cell RNA sequencing uncovers cellular diversity and rare populations by profiling individual cell gene expression and enabling differential expression analysis between cell communities and conditions. This service transforms biological samples into high-resolution data that advances research across diverse biological applications. 

Related:  10X, HIVE, Parse Biosciences

More info: Single-cell Sequencing

Proteomics:

Quantify relative protein expression levels using highly sensitive proximity extension assays across a variety of curated Olink panels containing biologically meaningful protein targets. Compare treatment groups using popular statistical methods to detect significant population level differences in expression for both high and low abundance proteins. 

Related: Olink HT, Olink Reveal, Olink Target

More info: Olink Proteomics

Methylation:

Differential methylation profiling can reveal meaningful insights into epigenetic mechanisms linked to your phenotypes of interest. Our analysis solutions utilise powerful statistical methods to investigate these patterns through annotated CpG sites (using the EPIC and Methylation Screening Arrays), and across the whole genome (EM-Seq, PacBio 5mC). 

Related:  Infinium arrays, Enzymatic Whole Genome Methyl-Seq, RRBS, PacBio

Ideal for researchers studying genetic disease, cancer, plant or animal breeding, or evolutionary change.

Discover the genetic differences that drive traits, disease, or performance. Our variant detection services identify SNPs, insertions, deletions, and other mutations across your samples, helping you pinpoint key changes that influence biology or health.

Somatic SR - WGS/WES ISO17025:

Somatic variant calling using DRAGEN to identify cancer-specific mutations, copy number alterations, and structural variants from whole genome or whole exome sequencing data with high sensitivity and specificity. This service transforms tumour and matched normal samples into comprehensive mutation profiles that support cancer biology research and drug discovery across cancer types. 

Related: Illumina WGS, Twist Exome Capture Panels

Germline/hereditary - ISO17025 Research uses, SNV, SV, CNV, Annotation, mitochondrial, HLA - SR and LGR:

Discover inherited and de novo variants in humans encompassing Single Nucleotide Variants (SNVs) and Insertion/Deletions (Indels), Copy Number Alterations (CNVs), as well as Translocations and other Structural Variants (SV). Annotated variants are provided from whole genome sequencing of short read (Illumina) or long read (PacBio) platforms, as well as targeted sequencing from panels.  

Related: Illumina WGS, Twist Exome Capture Panels, PacBio WGS

Pharmacogenomic - ISO17025 (Array, WGS, Long Read. CYP2D6, HLA):

Characterise drug-gene interactions through pharmacogenomic analysis. Star allele variant calling and annotation is provided through targeted array genotyping, short read WGS and panel based long read sequencing. All platforms include CYP2D6 and HLA haplotypes. 

Related: GDA+ePGx, Twist PGx Panel PacBio, Illumina WGS

Polygenic Risk Score analysis:

Partnering with Allelica, AGRF can provide Polygenic Risk Score (PRS) analysis of 20 common complex diseases. Linking risk scores to thousands of disease-associated variants facilities the calculation of an individual’s relative risk score of developing that disease compared against the general population. 

Related: Global Screening Array, Illumina WGS

Non-human variant calling:

Advance your research across any species with AGRF’s flexible non-human variant analysis service. Designed for agricultural, environmental, and model organism studies, these workflows deliver high-accuracy detection of SNVs, indels, and structural variants from Illumina or PacBio sequencing data. Using your supplied reference genome and annotations, AGRF provides fully customised analyses tailored to your species, data, and research goals. 

Related: Illumina WGS, PacBio WGS

Sanger Primer Designs:

Sanger primer design provides optimised primer sequences for targeted sequencing using the Sanger sequencing approach. These primers enable accurate validation of genetic variants, small insertions and deletions for variant confirmation, and targeted gene analysis. The optimal primers are designed and then ordered for use by our in-house Sanger sequencing team. 

Related: Sanger sequencing

Clinically (ISO15189) accredited services:

Germline/hereditary SR- ISO15189 clinical accreditation:

Providing clinical grade germline variant calling of Single Nucleotide Variants (SNVs) and Insertion/Deletions (Indels) using state-of-the-art methods. Using the Illumina DRAGEN framework, we provide highly accurate and expedited results. Assays include whole genome sequencing and targeted panel of protein encoding regions (exome) 

Related: Illumina WGS, Twist Exome Capture Panels

Somatic SR - TSO500 ISO15189, gene fusions:

Somatic analysis using the Illumina TSO500 platform detects mutations, fusions, copy number variants, tumour mutational burden, and microsatellite instability across ~500 cancer-relevant genes with targeted high-depth sequencing. This service transforms tumour samples into comprehensive genomic profiles that support cancer biology research and biomarker discovery for precision medicine applications. 

Related: Illumina WGS, Twist Exome Capture Panels

At AGRF, we help researchers understand the genetic makeup of individuals and populations. Genomic characterisation involves mapping and analysing the DNA of organisms to reveal their unique genetic features. Population genomic structure examines how genetic variation is distributed across groups, populations, or species, providing insights into ancestry, diversity, and evolution. Together, these analyses support research in fields such as agriculture, conservation, health, and personalised medicine.

Large genome and transcriptome assembly:

Accurate assembly of large and complex genomes or transcriptomes provides the foundation for functional and comparative genomics. Our pipelines integrate long-read (PacBio HiFi, ONT) and short-read (Illumina) data to generate high-contiguity assemblies with superior accuracy. For transcriptomes, we reconstruct full-length isoforms, assess expression diversity, and support downstream annotation. 

Related: PacBio HiFi, PacBio Iso-seq, Illumina Total RNA, ONT

Plasmid/small genome assembly and annotation:

We provide high-quality assembly and annotation of plasmids and small genomes, enabling insights into antimicrobial resistance, virulence, and mobility. Using long-read, short-read, or hybrid data, we generate complete, circularised sequences with detailed gene content characterisation. 

Related: PacBio HiFi, Oxford Nanopore, Illumina PE

Eukaryotic Genome assembly and annotation: 

We offer end-to-end workflows for assembling and annotating eukaryotic genomes, from contig construction and scaffolding (HiFi, Hi-C) to structural and functional annotation (genes, repeats, non-coding RNAs). Our solutions combine ab initio prediction, evidence-based transcript alignment, and protein homology for accurate gene model creation across a wide range of species. 

Related: PacBio HiFi, Omni-C/Hi-C, Illumina Total RNA

Long read transcript isoform assembly:

With PacBio’s long read sequencing method, RNA transcripts can be sequenced in their entirety. This avoids common concerns with aligning short-read data across exon junctions to accurately resolve complex splice events and detect novel transcript isoforms. 

Related: PacBio IsoSeq

Gene Editing & Transgenic changes:

Confirm the presence of transgenic nucleotide content in autosomal DNA through whole genome sequencing and our tailored bioinformatic approach. Alternatively, screen and exclude off-target editing events after applications such as CRISPR-Cas9. 

Related: Illumina WGS, PacBio WGS, Amplicon Sequencing

AGS: Hi-C: 

Hi-C captures 3D genome organization by identifying physical interactions between chromatin regions. Our analysis solutions use normalised contact maps and interaction matrices to investigate chromosomal loops, compartments (A/B), and topologically associated domains (TADs) at various resolutions. 

Related: Hi-C, Omni-C, in situ Hi-C, Arima-HiC

Micro-C: 

Micro-C enables high-resolution 3D genome mapping, detecting chromatin interactions at the nucleosome level. Using micrococcal nuclease digestion, Micro-C offers superior detection of fine-scale features such as promoter-enhancer loops and TAD boundaries — particularly in compact genomes or regulatory studies. 

Related data: Micro-C

Advanced Genomic Services:

Omni-C: 

Omni-C combines the best of Hi-C and ATAC-seq by utilising a DNase-based fragmentation approach to reduce bias and improve uniformity across the genome. It provides improved contact maps, especially in regions with inaccessible chromatin or high sequence complexity.  

Related: Omni-C (Dovetail)

CUT&RUN:

CUT&RUN (Cleavage Under Targets & Release Using Nuclease) is a high-sensitivity method for mapping protein-DNA interactions such as transcription factor binding or histone modifications. Our workflows produce high signal-to-noise profiles with minimal input material and reduced background. 

Related: CUT&RUN, CUT&Tag, ChIP-seq, ChIL-seq

ATAC-seq:

ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) maps open chromatin regions across the genome. This technique enables the profiling of regulatory elements, nucleosome positioning, and transcription factor footprints with low input material and rapid turnaround. 

Related: ATAC-seq, Omni-ATAC, Single-cell ATAC-seq (scATAC)

Allegro Targeted Genotyping V2 - Reference-based scalable target genotyping: 

Tecan Allegro Targeted Genotyping V2 combined with Illumina sequencing is a reference-based scalable approach to efficiently detect targeted variants across multiple genomic regions of interest. 

Related: SNP genotyping, Single Primer Enrichment TechnologyTM

Population Genomics - Genotyping by Sequencing (GBS): 

Genotyping by Sequencing (GBS) is a cost-effective, high-throughput approach for discovering and genotyping genetic variants in genomes with or without a reference sequencing. A wide range of restriction enzymes are available to tailor the genomic digests for specific species that will enable efficient genome-wide variant detection in population genomics studies and non-model or understudied species. This approach is ideal for SNP discovery, genotyping and genetic diversity analysis. 

Related: SNP genotyping, targeted sequencing

At AGRF, we help researchers explore the communities of microorganisms that live in and around us. Microbiome bioinformatics involves analysing complex microbial data to understand which microbes are present, how they interact, and how they influence health, disease, or the environment. These insights can guide research in medicine, agriculture, ecology, and beyond, unlocking the hidden impact of microbes on our world.

Gene targeting for taxonomic annotation using 16S, ITS, CO1, or custom primers on request: 

Profile microbial and eukaryotic communities through PCR-based sequencing of marker genes such as 16S, ITS or CO1. This approach enables taxonomic classification of specialised taxa or study-specific taxa. 

Related: Illumina Diversity Profiling, Pacbio 16S/ITS, dada2, ASV 

Taxonomic and functional characterisation using MetaWGS: 

Uncover the microbial composition of your microbial community with whole metagenome sequencing, short MetaWGS. This approach identifies organisms present, including bacteria, fungi and viruses, and functions supporting studies in health, agriculture and environmental monitoring.  

Related: Illumina WGS, kraken and bracken for taxonomic, human for functional annotation 

Metagenome contig assemblies through long-read: 

Generate high-quality metagenome assemblies using PacBio’s long read sequencing approach. This approach overcomes the limitations of short-read assemblies by spanning repetitive regions and resolving complex microbial genomes.   

Related: PacBio, MAGs, binning 

Functional screening: 

Identify genes or protein families linked to antibiotic resistance or genes of interests through sequence similarity to reference databases or specific sequences. By comparing metagenomic or genomic sequences against know functional and resistance gene databases, this approach enables in-silico detection of antimicrobial resistance genes, virulence factors and other relevant targets  

Related: AMRPlus, antimicrobial resistance profiling, carbohydrate-active enzymes 

Differential abundance analysis: 

Compare microbial taxonomic profiles across sample groups to identify taxa that differ significantly in abundance. This analysis reveals taxa associated with specific conditions, treatments or environments. 

Related: Deseq2, ancom, lefse, maslin 

Overall community structure analysis (alpha/beta diversity): 

Evaluate microbial community composition and diversity within (alpha) and between (beta) samples. Alpha and beta diversity metrics highlight community richness, evenness and diversity, providing insight into variation between groups. 

Related: vegan, PCoA, Shannon, Simpson, richness, evenness