Collection of applied bioinformatics and adjacent engineering repositories spanning variant triage, sequence alignment, genomics data parsing, qPCR quality control, and lab-operations tooling.
The active projects below include runnable code, example inputs, and documentation describing the underlying method.
ClinVar-first small-variant triage and reporting tool for research-oriented review workflows.
- Parses VCF input and performs assembly-aware ClinVar matching
- Surfaces conflicting interpretations and submission evidence
- Applies transparent ranking and emits HTML/CSV/JSON outputs
- Optional PharmGKB enrichment for PGx context
Repository: https://github.com/Maxim-Firsov/variant-review-workbench
Deterministic qPCR quality-control pipeline with HMM-style state calling and auditable outputs.
- Ingests RDML or canonical curve CSV
- Performs deterministic amplification-state inference
- Applies QC rules including NTC contamination and replicate discordance
- Emits CSV/JSON/HTML artifacts for review and audit
Repository: https://github.com/Maxim-Firsov/qpcr-quality-control
Pairwise sequence alignment project with both CLI and API surfaces.
- Dynamic programming implementation for global and local alignment
- Adjustable match, mismatch, wildcard, and gap scoring
- Linear and affine gap models plus alignment statistics
Repository: https://github.com/Maxim-Firsov/pgx-sequence-aligner
VCF processing utility that turns raw records into tabular summaries.
- Parses
GENE,IMPACT, andTRANSCRIPTannotations - Supports gzipped input and structured CSV/JSON exports
- Produces gene-level and variant-type summaries
Repository: https://github.com/Maxim-Firsov/genomic-variant-parser
Classical computer-vision pipeline for generating subject masks from video.
- Auto profile for practical 4K processing plus background subtraction
- Mask cleanup, component filtering, and GrabCut refinement
- Emits run metadata describing the exact processing configuration
Repository: https://github.com/Maxim-Firsov/foreground-matting-video-mask
Plate transfer validation utility focused on operational quality checks in wet-lab workflows.
This repository is not part of the current live portfolio rotation.
- Audits source-to-destination mapping consistency
- Detects transfer mismatches and rule violations
- Produces structured findings for downstream review
Repository:
- not public at current date
Project licensing is explicit at the repository level:
bioinformatics-portfolio: MITforeground-matting-video-mask: MITgenomic-variant-parser: MITpgx-sequence-aligner: MITplate-transfer-audit: MIT, inactive draftqpcr-quality-control: MITvariant-review-workbench: Apache License 2.0