DNA Sequencing Data Analysis

DNA sequencing enables identifying mutations, assembling genomes, and studying genetic variation in populations of any species. Our comprehensive DNA-seq analysis services cover the full spectrum from quality control to biological interpretation, delivering variant calls, annotations, and insights ready for downstream analysis or clinical decision-making.

We analyze DNA sequence data from:

Whole genome sequencing (WGS) — Complete genome analysis for variant discovery, structural variant detection, and genome-wide association studies
Whole exome sequencing (WES) — Focused analysis of coding regions for efficient variant discovery in disease research
Targeted sequencing panels — Custom and commercial panel analysis for specific gene sets or pathways
SNP arrays and genotyping — Population genetics, GWAS, and ancestry analysis
Metagenomic experiments — Microbial community analysis, taxonomic profiling, and functional annotation
Long-read sequencing (PacBio/Oxford Nanopore) — Isoform detection, structural variant calling, and de novo assembly
Structural variant analysis — CNV, translocation, inversion, and complex rearrangement detection
Variant calling & annotation — SNV/indel calling with functional annotation, pathogenicity prediction, and clinical interpretation

Deliverables: Variant call files (VCF), annotated results, quality metrics reports, visualization dashboards, and interpretation-ready summaries for clinical or research applications.

RNA Sequencing Data Analysis

Transcriptome-wide expression analyses are the standard approach to study molecular mechanisms in biological systems from single cells to complex microbiomes. We provide comprehensive RNA-seq analysis services that go beyond basic differential expression to uncover regulatory networks, identify biomarkers, and reveal mechanisms of disease or treatment response.

We analyze data from:

Bulk RNA-seq & differential expression — Identify differentially expressed genes across conditions with robust statistical methods and multiple testing correction
Single-cell RNA-seq (scRNA-seq) — Cell type identification, trajectory analysis, and cellular heterogeneity characterization
Small RNA-seq (miRNA, siRNA) — microRNA profiling, target prediction, and regulatory network analysis
Isoform quantification (Iso-Seq) — Full-length transcript analysis using long-read sequencing data
Alternative splicing analysis — Detect and quantify alternative splicing events, exon usage, and transcript isoform switching
Time-course and multi-condition studies — Longitudinal analysis, treatment response profiling, and dynamic expression patterns
Functional enrichment & pathway analysis — GO, KEGG, Reactome, and custom pathway enrichment to interpret biological significance

Deliverables: Expression matrices, differential expression results, pathway enrichment reports, publication-ready visualizations, and interactive exploration notebooks (R/Python).

Single-Cell & Spatial Transcriptomics

Single-cell RNA sequencing enables cataloging cells at a scale and resolution unmatched by bulk sequencing. Spatial transcriptomics provides a molecular view of the organization of complex tissues, revealing how cellular composition and gene expression vary across tissue architecture. Our analysis services help you discover rare cell types, map cellular trajectories, and understand spatial organization in health and disease.

We analyze:

Single-cell RNA-seq (scRNA-seq) — 10x Genomics, Drop-seq, Smart-seq2, and other platforms with quality control, normalization, and clustering
Spatial transcriptomics (10x Visium, MERFISH, etc.) — Spatial gene expression mapping, tissue architecture analysis, and region-specific expression patterns
Multi-omics integration (scATAC-seq, CITE-seq) — Integrate transcriptome, chromatin accessibility, and protein expression data for comprehensive cell characterization
Cell type identification & annotation — Automated and manual cell type annotation using reference datasets and marker genes
Trajectory and pseudotime analysis — Reconstruct cellular differentiation trajectories, identify branch points, and map developmental processes
Cell-cell communication analysis — Identify ligand-receptor interactions, signaling pathways, and intercellular communication networks
Cross-platform data integration — Harmonize data from multiple single-cell platforms or batch correction for multi-study analyses

Deliverables: Processed count matrices, cell type annotations, trajectory plots, spatial expression maps, interactive visualizations (CellxGene, Shiny apps), and comprehensive analysis reports.

Epigenomic Data Analysis

Epigenomics characterizes the chromatin state down to minuscule chemical modifications, providing deeper understanding of gene regulation and biomarkers for diseases. Our epigenomic analysis services help you map regulatory landscapes, identify enhancers and promoters, and understand how chromatin modifications control gene expression in development, disease, and treatment response.

We analyze:

ATAC-seq (chromatin accessibility) — Identify open chromatin regions, active enhancers, and regulatory elements genome-wide
ChIP-seq & CUT&RUN (protein-DNA interactions) — Map transcription factor binding sites, histone modifications, and chromatin-associated proteins
DNA methylation (WGBS, RRBS) — Genome-wide and targeted methylation profiling for biomarker discovery and regulatory analysis
Histone modification analysis — Characterize H3K4me3, H3K27ac, H3K27me3, and other modifications to understand chromatin states
Chromatin state segmentation — Integrate multiple marks to define chromatin states (active promoters, enhancers, heterochromatin, etc.)
Regulatory element identification — Discover enhancers, promoters, insulators, and other regulatory sequences with functional annotation

Deliverables: Peak calls, bigWig tracks, chromatin state maps, differential accessibility/occupancy results, and integration with expression data to link regulatory elements to target genes.

Proteomic & Metabolomic Analysis

Proteomics and metabolomics reveal the functional state of a biological system, complementing genomic insights with protein and metabolite profiles. While genomics tells you what could happen, proteomics and metabolomics tell you what is happening. Our analysis services help you understand functional changes, identify biomarkers, and integrate multi-omics data for comprehensive biological insights.

We perform:

Mass spectrometry data analysis — Process raw MS data from LC-MS/MS, TMT, label-free, and other proteomics platforms
Protein identification & quantification — Database searching, FDR control, and quantitative analysis across conditions
Metabolite profiling & pathway analysis — Identify and quantify metabolites, map to metabolic pathways, and detect pathway dysregulation
Multi-omics integration — Integrate proteomic/metabolomic data with transcriptomic and genomic data to build comprehensive molecular models
Biomarker discovery — Identify protein or metabolite signatures associated with disease, treatment response, or clinical outcomes

Deliverables: Protein/metabolite quantification tables, differential abundance results, pathway enrichment analysis, multi-omics integration reports, and biomarker candidate lists with validation recommendations.

Workflow Engineering & Clinical-Grade Compliance

Production-grade pipelines and infrastructure with regulatory readiness. We don't just build analysis workflows—we engineer systems that are scalable, maintainable, and compliant. Whether you need research-grade pipelines or clinical systems that pass regulatory audits, we design with production requirements and compliance standards in mind from the start.

Our workflow engineering services include:

Nextflow pipeline development & containerization — Build reproducible, portable workflows using Nextflow with Docker/Singularity containers for consistent execution across environments
HPC cluster & cloud-native architectures (AWS) — Optimize for on-premise HPC clusters or design cloud-native solutions using AWS Batch, Step Functions, and Lambda for scalable processing
Scalable compute strategies (Batch/Step Functions/Lambda) — Implement cost-efficient compute architectures using Spot instances, auto-scaling, and right-sized resources to balance performance and cost
CLIA/CAP-aligned dry-lab bioinformatics — Design workflows that meet CLIA/CAP requirements for clinical laboratory testing, including validation, quality control, and documentation standards
GxP mindset, SOP-driven processes & validation — Develop standard operating procedures (SOPs), validation protocols, and change control processes aligned with GxP principles for regulated environments
Version control, traceability & audit-ready documentation — Implement Git-based version control, comprehensive logging, and documentation that supports regulatory audits and inspections
Hybrid on-prem + cloud deployments — Design flexible architectures that combine on-premise infrastructure with cloud resources, supporting data residency requirements and cost optimization

Deliverables: Production-ready pipelines (Nextflow workflows), container images, infrastructure-as-code (Terraform/CloudFormation), SOPs, validation documentation, deployment guides, and ongoing maintenance support.

Our Services