Bioinformatics

Our services

Bioinformatics

Bioinformatics & Analytical Modeling

At NIUM, we transform sequencing data into actionable insights by integrating end-to-end bioinformatics, advanced modeling, and tailored statistical analysis. Whether for standardized deliverables or deep dive research, our platform delivers clarity — across all scales of microbiome-focused projects:

Microbiome Report Projects
(Amplicon & WGS)

For clients seeking standardized reports

Automated workflows for high quality data processing, including quality control, taxonomic profiling, and functional gene annotation from 16S/18S amplicon or shotgun WGS.
Core ecological metrics (alpha/beta diversity, richness, evenness).
Targeted functional analysis of key pathways or genes of interest.
Concise, actionable reports—perfect for regulatory, marketing, or product assessment.

Client driven Projects (B2B Partnerships)

Customized bioinformatics pipelines aligned with business goals

Taxonomic and functional profiling (amplicon & WGS).
Ecological metrics, including diversity analysis.
Hypothesis-driven statistical investigation: differential abundance, association testing, correlation networks.
Focus on community-level structure, species of interest, and integrating multiomics (e.g. metabolomics).
Resolution tuned to medium-to-high, pinpointing specific species or strains.

Research Grade Projects

For clients needing full-depth exploration and discovery

All standard steps plus:

Genome-resolved metagenomics: MAG recovery, genome binning, and curation.
Mobile genetic element detection: prophage, plasmid, transposon identification.
Strain-level tracking and SNV analysis.
Advanced ecological modeling, including niche modeling and community interaction networks.
Integrated multiomics statistical frameworks, with machine learning or network-based analysis.
Reproducible, fully-documented pipelines – ideal for publication, collaboration, or regulatory use.

Why Choose NIUM’s Pipeline?

Sequential data

Amplicon (16S, 18S)
Shotgun Metagenomics (WGS DNA)

Bioinformatics processing

Quality check
Taxonomy profile
Functional profile
Track, specific species, functions, etc (on-demand)

Downstream analysis

Metadata processing
Statistical analyses
Modeling
Custom analysis available (on-demand)

Automated & Scalable

Handles 10s to 1,000+ samples with consistent quality.

Flexible Customization

From core analyses to bespoke, hypothesis-driven workflows.

Integrated Shotgun & Amplicon

Comparative power of taxonomic + functional insights.

MultiOmics Enabled

Supports metabolomics, proteomics, and metadata integration.

DepthDriven Resolution

Choose the right detail—community overview or strain-level precision.

Ecological & Metabolic Modeling

From diversity metrics to network inference and community simulation.

Publication-Ready

Full documentation, version control, and outputs ready for scientific or regulatory use.

Deliverables & Outputs

Automated Quality Report: QC metrics, rarefaction, contamination checks.

Taxonomic Overview: Graphs, heatmaps, abundance tables.
Functional Profile: Pathway abundances, CAZy, BGCs where relevant.
Ecological Metrics: Diversity trends, betadiversity PCoA/PCAs, PERMANOVA.
Statistical Insights: Volcano plots, differential abundance results.
Advanced Analysis: Microbial networks, MAGs, mobile element profiles.
MultiOmics Integration: Correlations, multivariate stats, machine learning models.
Comprehensive Report: Visualizations and interpretations fit for strategy, scientific publication, or regulatory use.

Integrations with InVitro & Other Platforms

Our bioinformatics workflows dovetail seamlessly with NIUM’s IMAT in-vitro platform. Metabolomic, pH, and host-cell data are integrated to:

Validate predictions from metabolic modeling.
Map microbial changes across gut compartments.
Build predictive models linking interventions — like probiotics or ingredients — to microbiome shifts.