NGS Data Analysis

NextGen Sequencing Analysis Solutions in Africa

Metagenomics is the study of genetic material from a community of microbial organisms directly recovered from environmental samples in their natural state

Our comprehensive NGS analysis pipeline involves the quality control of raw reads, pre-processing, mapping, post-alignment processing, variant calling, and annotation and prioritization of variants. We conduct analysis of whole genome, whole exome, RNASeq, and targeted NGS data, leading to discovery of germline single nucleotide polymorphisms (SNPs), indels, structural variants (SVs), and copy number variants (CNVs); somatic SNVs, SVs, and indels, and RNASeq SNPs and indels.

Outputs include: SAM, BAM, and VCF files and a list of SNPs.

Storage period of your files: 3 months.

core microbiome

Metagenomics Data Analysis

Our metagenomics analysis pipeline reveals the abundance and diversity of microbes at the genus and species level, and maps correlations between different species/populations

We provide a detailed analysis of 16srRNA and 18srRNA, ITS and shotgun metagenome data. This analysis aids in the understanding of the interactions between microbes and their hosts, identification of active pathways, discovery of how microbial gene expression impacts host disease onset and progress, among others

Visual ExplorationAbundance ProfilingStacked bar / area plot, Interactive pie chart, Rarefaction curves, Phylogenetic tree, Heat tree analysis, FB Ratio
Microbial community profilingAlpha Diversity AnalysisChao 1 Index, ACE, Shannon, Simpson, & Fisher indices
T-test/ANOVA p-value & T-statistic, Mann-Whitney/Kruskal-Wallis p-value & Mann-Whitney statistic
Beta Diversity AnalysisPCOA plot, PERMANOVA, ANOSIM, & PERMDISP statistics
Core Microbiome AnalysisHeatmap and Results Table
Clustering & CorrelationHeatmap ClusteringHierarchical Clustering & Heatmap Visualization
Dendrogram AnalysisTree based on unweighted Unifrac distance
Correlation AnalysisSparCC correlation tables, network, and boxplots
Comparison and ClassificationClassical univariate analysisT-test/ANOVA p-value & T-statistic, Mann-Whitney/Kruskal-Wallis p-value & Mann-Whitney statistic
MetagenomeSeqZero inflated Gaussian fit: p-values and FDR values
Differential Abundance Analysislog2FC, logCPM, P-values, and FDR values
LEfSe AnalysisLDA scores, p-values, FDR values, analysis results table
Random Forest AnalysisMDA Accuracy, OOB error rates, RF plots, important features


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Expert Bioinformatics Analysis

PhD-level bioinformatics analysis is bundled with the sequencing services and involves:

  • Alpha diversity analysis
  • Beta diversity analysis
  • Core microbiome analysis
  • Phylogenetic analysis
  • Heatmap clustering
  • Univariate analysis - METASTATS, LefSE, T-test/ANOVA,
  • Random forest classification
  • Taxon set enrichment analysis (TSEA)
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Metagenomic Sequencing Features & Overviews

  • Long reads

    long read sequencing resolves structural variants, repeat regions and phasing with long reads.

  • Direct Sequencing

    Direct RNA sequencing eliminates bias, allowing for a comprehensive assessment of epigenetic modifications

  • DNA Sample Collection Instructions

    Sample collection instructions

  • Microbial DNA

    Pathogens can be detected accurately and strains typed precisely.

  • Short Turnaround Time

    Results are available in 10 working days.

  • Confidentiality

    Client information is held in struct confidence and all data is returned to the client or discrded unlesss the client asks us to store it.


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