Bioinformatics

• Key advantages

• Robust data processing pipelines for sequencing and proteomics data

• Accurate variant calling, annotation, and prioritization for genomic analyses

• Fully integrated platform combining sequencing, interpretation, and decision support

• Customizable workflows tailored to research, clinical, and translational needs

• Integration of multi-omics datasets for holistic biological interpretation

• Proprietary tools: AVANTI (analysis), EXTENSA (clinical insights), Dante DB (reference data)

• Phenotype-driven analysis linking genomic data to clinical or experimental outcomes

• AI-guided interpretation prioritizing clinically relevant regions per sample

• Seamless workflow from raw data to report generation, without external software

• Scalable cloud-based solutions ensuring high-performance computing and data security

• Continuously enriched whole-genome database supporting longitudinal studies and variant curation

• Interactive visualization tools for easy exploration of complex datasets

• Support for AI/ML applications in variant interpretation and biomarker discovery

• Optimized for clinical, research, and large-cohort applications

Technical specifications

• Data types supported: WGS, WES, RNA-seq, single-cell sequencing, proteomics, epigenomics, metagenomics

• Platform components:

              – AVANTI: Web-based tool for raw data processing and report generation (FASTQ → VCF → report)
              – EXTENSA: AI-powered engine for clinical annotation, phenotype integration, and risk modeling
              – Dante DB: Continuously updated whole-genome and medical data reference database

• Data compatibility: FASTQ, BAM, VCF, gVCF from any NGS platform

• Workflow management: Modular, reproducible pipelines via Nextflow, Snakemake, CWL; Docker/Singularity support

• Quality control modules: FastQC, MultiQC, Qualimap, Picard for multi-stage QC

• Alignment and mapping: BWA-MEM, Bowtie2, STAR, Minimap2 (long-read)

• Variant detection: GATK, FreeBayes, DeepVariant (SNVs/indels); Manta, LUMPY, Delly (SVs); CNVkit, ExomeDepth (CNVs)

• Transcriptomics analysis: Salmon, Kallisto, RSEM + DESeq2, EdgeR, limmaSalmon, Kallisto, RSEM + DESeq2, EdgeR, limma

• Single-cell bioinformatics: Cell Ranger, Scanpy, Seurat for clustering and trajectory inference

• Proteomics workflows: MaxQuant, Proteome Discoverer; peptide quantification and functional annotation

• Epigenetics: Bismark, MACS2, DiffBind for methylation (WGBS/RRBS) and ChIP-seq

• Multi-omics integration: WGCNA, pathway enrichment (KEGG, Reactome), ML-based feature selection

• Annotation databases: ClinVar, gnomAD, dbSNP, HGMD, COSMIC, CADD, PolyPhen, SIFT

• AI modules:

              – Dynamic region prioritization per individual
              – Predictive modeling for variant significance
              – Feedback loop to lab for sequencing optimization

• Cloud computing: Scalable on AWS, Google Cloud, Azure with Kubernetes orchestration

• Output formats: VCF, BAM, FASTQ, expression matrices, interactive reports (HTML/PDF), LIMS integration

• Output content: Annotated VCFs, variant summaries, dashboards, and clinical-grade reports (carrier screening, oncology, rare diseases, PGx, etc.)

• Data security and compliance: GDPR, HIPAA, ISO-aligned infrastructure with encryption, user authentication, and audit trails

• Scalability: Designed for both individual clinical cases and population-scale projects