Bioinformatics

Expert bioinformaticians analyze NGS data to maximize your project’s potential

NGS Data Analysis Services

Admera Health expert team with extensive experience empowers researchers with informative results with ready to review reports along with expert support. Admera Health’s accomplished bioinformaticians provide comprehensive support and customized solutions to enhance the effectiveness of our clients’ research.

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Genomic Analysis

  • Standard Analysis:

    QC, Alignment, Duplicate Marking, Germline/Somatic Variant Detection and Functional Annotation

    Optional Analysis:

    Structural Variation and CNV detection

    Low Pass WGS Imputation and genotyping

    Tumor Fraction estimation in cell-free DNA

    Host-Vector Insertion detection

    PDX read cleaning

  • Standard Analysis:

    QC, De novo Assembly, Assembly Stats

    Optional Analysis: For Bacterial Isolates Only

    Taxonomy assignment, MLST, Antimicrobial resistance analysis

    Pangenome analysis

    Plasmid replicons screening

    Serotyping (only for Escherichia and Salmonella)

    fimH-Typing (only for Escherichia)

    Subtyping (only for Klebsiella)

  • Standard Analysis:

    QC, Alignment, Duplicate Marking, Germline/Somatic Variant Detection and Functional Annotation

    Optional Analysis:

    Somatic Structural Variation and CNV detection

    Tumor Mutation Burden (TMB) Estimates

    HLA Typing

    Microsatellite Instability (MSI) prediction

    Neoantigen Prediction

  • See Whole Exome Sequencing - WES (Hybrid Capture)

  • Standard Germline Sample Anayses: Assembly Stats, Contig, Scaffolds, Intermediate files

    Taxonomy assignment using The Genome Taxonomy Database (GTDB) (for microbiome only)

    Scaffolds Annotation (For Genome < 10MB Only)

    Other/Additional Customized Analysis

Transcriptomic Analysis

  • Standard Analysis:

    QC, Alignment, Gene Feature counts & Normalization

    Optional Analysis:

    Differential Expression Analysis

    GO Enrichment & KEGG Analysis

    ANNOVA Analysis

    Alternative Splicing Events detection

    Interaction Network Analysis

    RNA Variant detection

    RNAs Structures and Shapemapper Signatures analysis

  • QC and trim adaptors

    Mirdeep2 miRNA analysis and DE downstream analysis

    COMPOSA miRNA, circRNA, snoRNA, piRNA, snRNA and tRNA quantification and DE downstream analysis

  • Standard Analysis:

    QC, read correction, unfixable read cleaning, Trim & Remove Overrepresented sequences, Assembly and Annotation

    Optional Analysis:

    Trinity assembly

    Assembled transcription annotation

    RSEM Analysis

    DE Analysis

    GO Enrichment Analysis

Microbiome Analysis

  • Standard Analysis:

    Qiime QC, Taxonomy & Feature/OTU Tables

    Optional Analysis:

    Feature/OTU Heatmap & Bar plots

    Alpha Diversity Analysis (Diversity indices, Rarefaction curve, Rank-abundance plot)

    Beta Diversity Analysis (Distance matrix, PCA plot, UPGMA tree)

    Differential Analysis (Differential heat tree, ANOSIM analysis, Meta stats analysis)

    Sample Pathway Abundance prediction

  • Standard Analysis: Qiime QC, Taxonomy & Feature/OTU Tables

    Optional Analysis:

    Feature/OTU Heatmap & Bar plots

    Alpha Diversity Analysis (Diversity indices, Rarefaction curve, Rank-abundance plot)

    Beta Diversity Analysis (Distance matrix, PCA plot, UPGMA tree)

    Differential Analysis (Differential heat tree, ANOSIM analysis, Meta stats analysis)

    Sample Pathway Abundance prediction

  • Standard Analysis:

    Qiime QC, Taxonomy & Feature/OTU Tables

    Optional Analysis:

    Feature/OTU Heatmap & Bar plots

    Alpha Diversity Analysis (Diversity indices, Rarefaction curve, Rank-abundance plot)

    Beta Diversity Analysis (Distance matrix, PCA plot, UPGMA tree)

    Differential Analysis (Differential heat tree, ANOSIM analysis, Meta stats analysis)

    Sample Pathway Abundance prediction

    De novo assembly, Gene prediction and Functional annotation (Metagenomic only)

  • Standard Analysis:

    QC, Trimming, Alignment, rRNA sequence separation

    Optional Analysis:

    Taxonomy Assignment/Genus identification

    Community Profiling

    Diversity Analysis

    Functional Annotation (KEGG)

Epigenomic
Analysis

  • Standard Analysis:

    QC, Read Trimming, Alignment, Duplicate Removal (WGBS Only), Extract Methylation (CX report)

    Optional Analysis:

    Differential Methylation Analysis (CpG and Non-CpG)

    DE gene annotation

  • Standard Analysis:

    QC, Read Trimming, Alignment, Duplicate Removal (WGBS Only), Extract Methylation (CX report)

    Optional Analysis:

    Differential Methylation Analysis (CpG and Non-CpG)

    DE gene annotation

  • Standard Analysis:

    QC, Alignment, Duplicate Removal (WGBS), Extract Methylation (CX report)

    Optional Analysis:

    Differential Methylation Analysis (CpG and Non-CpG)

    DE gene annotation

  • Standard Analysis:

    QC, Alignment, Duplicate Removal, MT reads Filtering, IQR Plots

    Optional Analysis:

    Peak Detections, TSS annotations and Peak enrichment analysis

    Differential Binding Analysis

    DB annotation

    GO Enrichment and KEGG Analysis

  • Standard Analysis:

    QC, Alignment, Sample Correlation, Peak Detection

    Optional Analysis:

    Differential Binding Analysis

    DB annotation

    GO Enrichment and KEGG Analysis

    Motif Analysis

    Aggregated Density Profile Analysis

  • Standard Analysis:

    QC, Alignment, Spike-in Normalization, Sample Correlation, Peak Detection

    Optional Analysis:

    De novo Motif Identification and Motif Foot printing

    Differential Binding Analysis

    DB annotation

    GO Enrichment and KEGG Analysis

    Aggregated Density Profile Analysis

  • Standard Analysis:

    QC, Alignment (Juicer), Contact statistics, Contact domains

    Optional Analysis:

    Chromatin Loop Detection and Scaffolding analysis

Single-Cell Analysis

  • Standard Analysis: QC, Mapping, Cluster t-SNE projections, Cluster stats

    Optional Analysis:

    Violin plots for number of genes, UMIs, and %Mito of each cell

    Single Cell vs VDJ Analysis

    Cell type Analysis of Marker Genes (Dot plots, Count table, Bar Plots, t-SNE/UMAP Annotation),

    GO Enrichment and KEGG Analysis

    Pseudotime Analysis

  • VDJ Standard Analysis:

    VDJ enrichment, expression, and annotation

    VDJ Optional Analysis:

    Top 10 clonotype frequency and CDR3 sequences detection

    VDJ Clonotypes Diversity (Bar Plots of segments vs. CDR3 length & clono-types vs. CDR3 length),

    VDJ Clonotypes Overlapping (Heatmap of overlapping variable region & CDR3)

    Single Cell vs VDJ Overlapping (T/B cells, Fraction Table and Barplots of TSNE/UMAP cluster with VDJ)

    Cell type Analysis of Marker Genes (Dot plots, Count table, Bar Plots, t-SNE/UMAP Annotation)

  • Standard Analysis:

    QC, Filtering, Barcode Counting, transposase cut size detection accessible chromatin peaks detection, cell calling, count matrix generation , dimensionality reduction, cell clustering, and cluster differential accessibility

Spatial Transcriptome Analysis

  • Standard Analysis:

    Stereo-seq Analysis Workflow (SAW): QC & metrics statistics, Mapping, Tissue/Cell segmentation, Spatial UMAP & tissue clustering, Violin plots for gene & MID

    Optional Analysis:
    Single-Cell RNA-seq related analysis
    Customized requests

  • Standard Analysis:

    Space Ranger: QC & metrics statistics, Mapping, Tissue/Cell segmentation, Spatial UMAP & tissue clustering, Violin plots for gene & MID

    Optional Analysis:
    Single-Cell RNA-seq related analysis 
    Customized requests

Customized Analysis

We would love to hear about your research so our expert team of scientists can build a pipeline to meet your requirements.

Advantages of Working with Admera Health

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Mature Pipelines

Carefully curated pipelines deliver reliable data in industry-leading turnaround time

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Expert Scientific Support

Experienced team with mature pipelines and customizable workflows

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Proven Quality Service

Technical support during analysis and after data analysis results are delivered

Other Services That Might Be of Interest

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Transcriptomics

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Single-Cell Sequencing

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Bioinformatics