Pakistan SARS-CoV-2 Nextstrain Dataset

This repository hosts the generated Auspice JSON files for the Pakistan SARS-CoV-2 Nextstrain community build.

• Public Nextstrain build: https://nextstrain.org/community/NIH-BIGVI-PAKISTAN/ncov/Pakistan
• Reproducible build workflow: https://github.com/adnanhaider81/pakistan-sars-cov-2-nextstrain-build

Repository Purpose

Nextstrain community builds can be served directly from GitHub repositories. This repository is the publishing location for the Pakistan SARS-CoV-2 dataset.

The files in auspice/ are generated by the Nextstrain ncov workflow and are read by Nextstrain to display the public interactive phylogeny.

Files

auspice/ncov_Pakistan.json
auspice/ncov_Pakistan_root-sequence.json
auspice/ncov_Pakistan_tip-frequencies.json

These files contain the exported Nextstrain/Auspice dataset, root sequence information, and tip frequency information for the Pakistan build.

Build Workflow

The reproducible workflow, profile files, helper scripts, and step-by-step instructions are maintained here:

https://github.com/adnanhaider81/pakistan-sars-cov-2-nextstrain-build

In brief, the build process is:

1. Download Pakistan SARS-CoV-2 metadata and sequences from GISAID.
2. Run the official Nextstrain ncov workflow with the Pakistan profile.
3. Add a small open Nextstrain reference set for rooting and global context.
4. Export the Auspice JSON files.
5. Copy the generated ncov_Pakistan*.json files into this repository.
6. Commit and push this repository to update the public Nextstrain page.

Data Note

Raw GISAID FASTA and metadata files are not stored in this repository. GISAID data must be handled according to GISAID terms of use and applicable institutional policies.

Maintainer

NIH Bioinformatics Group of Virology, Pakistan.