Workflow stewardship
Versioned configuration, scripts, environments, tests, and release documentation support repeatable builds.
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Maintained public genomic-surveillance resource
Maintaining Pakistan’s SARS-CoV-2 Nextstrain Community Build.
I maintain the reproducible analysis and publishing workflow behind the NIH Bioinformatics Group of Virology’s Pakistan-focused public build—connecting quality control, time-resolved phylogenetics, responsible data handling, and interactive outbreak communication.
My role
Maintainer & workflow developer
Workflow release v0.1.1 · archived on Zenodo
- 28 Aug
- 2026 public dataset update
- 5,104
- sequences in the public tree after filtering and context selection
- 4,942
- Pakistan sequences retained in the final tree
- 162
- international sequences retained for context
Contribution
A maintained resource, not a one-off visualization.
The public build is presented institutionally by the NIH Bioinformatics Group of Virology, Pakistan. My contribution is the reproducible workflow and the publishing path that carries a reviewed build from controlled inputs to the institutional repository and then to the public Nextstrain Community view.
Analytical review
Sequence quality, metadata consistency, filtering decisions, phylogeny, and time structure are reviewed as one chain of evidence.
Public communication
Auspice turns the reviewed output into an explorable view while the written record preserves scope and interpretation limits.
Nextstrain Community builds are independently maintained resources hosted through GitHub. The wording here distinguishes this resource from datasets maintained directly by the Nextstrain team.
Reproducible workflow
From controlled inputs to a public phylogeny.
- 01
Prepare inputs
Locally held GISAID sequence and metadata files are mapped into the documented Pakistan build profile.
- 02
Review sequence quality
Nextclade quality signals and workflow filters identify records that do not meet the build criteria.
- 03
Select context
Pakistan sequences are combined with a bounded international context set for more careful interpretation.
- 04
Infer phylogeny
The Nextstrain SARS-CoV-2 workflow uses IQ-TREE to estimate the tree from the retained alignment.
- 05
Resolve time structure
TreeTime places genomic relationships on a temporal scale and supports the dated public view.
- 06
Publish with provenance
Auspice JSON is released through the institutional repository, with the reusable workflow versioned and archived separately.
Data governance
Open methods, responsible sequence handling.
Published openly
- Workflow configuration and scripts
- Environment and container definitions
- Release notes, documentation, and tests
- Public Auspice visualization outputs
Kept outside the code repository
- Raw GISAID sequence downloads
- Restricted or non-public metadata
- Credentials and local data paths
- Any input that cannot be redistributed
This separation makes the analytical method inspectable without representing access-controlled sequence data as unrestricted material. It also keeps the public repository usable as a reproducibility record.
Public records
Explore, inspect, and cite the work.
Interactive resourceExplore the live buildPhylogeny, dates, geography, and filters ↗
Reproducible methodReview the workflowConfiguration, scripts, tests, and releases ↗
Institutional publishing recordView the public build repositoryAuspice outputs served by Nextstrain Community ↗
Archived releaseCite version 0.1.1Permanent Zenodo record and DOI ↗
Research noteHow a phylogenetic build becomes a useful communication product
Read the field note →
Discuss the work