Portfolio Map
Pathogen Genomics Portfolio Map
A concise map of public repositories, methods areas, and the evidence each workflow gives to a reviewer, supervisor, collaborator, or remote bioinformatics employer.
| Area | Repository | What it proves |
|---|---|---|
| Poliovirus DDNS/ONT | DDNS MinION VP1 pipeline | ONT, VP1, DDNS, run review, barcode-folder analysis, HTML reporting. |
| Poliovirus Illumina | Whole-capsid NGS workflow | Illumina, consensus generation, antigenic-site summaries, phylogeny, surveillance reporting. |
| Phylodynamics | WPV1 phylogeography | R, tree dating, movement summaries, stochastic mapping, reproducible synthetic-data demo. |
| Metagenomics | Pathogen discovery pipeline | Host subtraction, competitive mapping, cautious interpretation, confirmatory evidence review. |
| Workflow engines | Viral genomics Nextflow demo | Nextflow DSL2 modules, Docker and SLURM profiles, CI smoke testing, toy FASTQ-to-report workflow. |
| Respiratory viruses | RSV workflow / SARS-CoV-2 workflow | Outbreak genomics, manuscript-linked pipelines, consensus, lineage/genotype calls, phylogeny. |
| Genomic dashboards | Pakistan SARS-CoV-2 Nextstrain build | Nextstrain configuration, curated metadata, Auspice JSON generation, and public outbreak communication. |
| Arboviruses/zoonoses | DENV workflow / CCHFV workflow | Serotype-aware dengue genomics and segment-aware CCHFV analysis with phylogeny and QC review. |
Research Evidence
Recent publications, resources, and peer review
Verified public outputs added to the portfolio during 2026.
| Output | Public record | Portfolio evidence |
|---|---|---|
| Influenza A(H3N2) genomic surveillance | Journal of Medical Virology, 2026 | Respiratory-virus surveillance, whole-genome sequencing, clade analysis, and public-health interpretation. |
| Integrated influenza, SARS-CoV-2, and RSV surveillance | Archives of Virology, 2026 | Multi-pathogen genomic surveillance linking RT-PCR screening, sequencing, and epidemiological interpretation. |
| Viral NGS traceability checklist | protocols.io, 2026 | Workflow quality, control review, version tracking, reportability decisions, and public-safe documentation. |
| Open peer review | 10 public PREreviews | Constructive review across pathogen genomics, wastewater surveillance, phylodynamics, and infectious-disease epidemiology. |