Portfolio · Projects
Software and analyses I have built
Pipelines, clinical genomics tools and analyses from my rare-disease work. Most of the code is private, so each project is shown with screenshots or a workflow overview. I’m happy to walk through any of them on a call.
Clinical genomics platforms
From raw reads to a reviewed, reportable result
VARDIGS + PgAD
A rare-disease interpretation platform linked to the Pakistan Genome Aggregate Database. Pakistani populations are badly under-represented in gnomAD, so local frequencies change how variants are classified.
- VARDIGS: case intake, HPO phenotype capture, VCF analysis, evidence-based prioritisation and clinical review.
- PgAD Admin: independent curation of de-identified assertions with structured ACMG/AMP evidence and a full audit trail.
- PgAD Browser: a public, read-only view of privacy-thresholded allele frequencies on GRCh37 and GRCh38.
- Raw VCFs, notes and identifiers never leave VARDIGS. Only de-identified aggregates cross into PgAD, through narrowly scoped tokens.
VARDIGS pipelines
Reproducible NGS pipelines with configurations for whole exome, whole genome, BRCA1/2 panels and a 58-gene myeloid panel, used for clinical and cohort analysis.
- FASTQ → uBAM → BWA-MEM → MarkDuplicates → BQSR → HaplotypeCaller, with a Mutect2 somatic branch.
- Hard filtering for SNPs and indels, annotation with Funcotator, ANNOVAR or VEP, and alignment QC metrics.
- Conda environments per rule, so every run can be repeated on a laptop, an HPC cluster or the cloud.
Genetic Report Builder
A report generator for sequencing labs. It turns a classified variant into a signed, multi-page clinical-style PDF.
- HPO term search, gene summaries from MyGene.info, and ACMG/AMP criteria with automatic classification.
- A draft → in review → approved → released workflow with four signatories.
- Supports NGS, Sanger or combined test types, and keeps a searchable dashboard of saved reports.
HbScribe
A locally hosted application for HBB Sanger traces. You upload AB1 files and get QC-filtered findings ranked by confidence. Every saved result can be re-analysed and exported as a traceable report.
- A chromatogram viewer for reviewing each call against the raw trace.
- Reports include the frozen assay profile and a verification hash.
- User accounts, a background worker, PostgreSQL, HTTPS and encrypted backups, deployed with Docker Compose.
For research use only.
Genomics LIMS
A laboratory information system for a service lab that offers DNA extraction, Sanger sequencing and NGS.
- Barcoded samples and batches, QC checkpoints and Illumina sample sheet export.
- Reagent lot and expiry tracking, plus PKR/USD invoicing with prices locked at sample receipt.
- Role-based access, field-level encryption of patient data and a complete audit trail.
Free tools on this site
Tools anyone can use
Pronto Primer
PCR primer design for any human variant. Enter a gene and an HGVS variant, coordinate or rsID. Pronto Primer resolves it on the recommended transcript, fetches the flanking sequence and designs primers with Primer3.
- Validates primer pairs with UCSC in-silico PCR.
- Experimental ARMS-PCR modes: two-tube and tetra-primer.
- Exports results as a PDF or HTML report.
ACMG Variant Classification Workbench
An educational tool for seeing how ACMG/AMP 2015 evidence codes combine into a classification. Toggle the evidence and the result and evidence balance update live.
Pedigree Pro
A browser-based pedigree drawing tool that follows standardised nomenclature. It handles partners, siblings, twins, consanguinity, carrier status and up to four phenotype quadrants, and exports to PNG.
Research software
Open-source tools and collaborations
ExScope
A command-line tool for coverage plots from BAM or CRAM files. It works on one gene, a batch of genes or a whole chromosome, and draws strand-aware coverage with exon tracks.
inTRuder
I participated in the BCM × DNAnexus Hackathon 2026 as part of the team that built inTRuder, a tool for identifying novel tandem-repeat loci and motifs in individuals that are not in the reference genome.
Analysis showcases
Selected analyses
16S rRNA metagenomics pipeline
A 24-job Snakemake pipeline that runs QIIME 2 through Docker. It covers DADA2 denoising, taxonomy, phylogeny, core diversity metrics and alpha-diversity correlations, and includes setup and preflight scripts.
RNA-seq differential expression
Differential expression of SARS-CoV-2-positive versus negative nasopharyngeal swabs from public GEO data. Covers count import, metadata matching, DESeq2 modelling and MA, volcano and top-50 heatmap visualisations.
Molecular dynamics
A GROMACS molecular dynamics pipeline run from a Jupyter notebook, with ready-made parameter templates and a step-by-step guide.
Need something similar? Tell me what data you have and what you want to find out, and I’ll suggest a practical plan. Contact me on Upwork →