Nextstrain uses Auspice to visualize JSON files that are created by Augur. Here we share our instance via community on gitgub.
This instance includes 1970 genomes sampled between March 2021 and November 2021. We only selected samples with high-coverage complete genomes (above 29,000 bp) from GISAID. According to GISAID, high coverage means that only entries with less than 1% of undefined bases (NNNs) and no insertions and deletions unless verified by the submitter are tolerated.
There are 981 samples collected from Texas, 327 of which are focused on Harris county (Houston). Through collaboration with the Houston Health Department, we acquired the detailed metadata of all these Texas samples, including zip code, sex, and race. To investigate when and how did SARS-CoV-2 circulate in Houston, we also collected worldwide samples as 'background'. In total, 392 samples were collected in other US states (except Texas); 100 samples were collected in North America (except the USA); 99 samples were collected in South America; 100 samples were collected in Europe; 100 samples were collected in Asia; 98 samples were collected in Africa; 100 samples were collected in Oceania.
The following plot showed the collection date of all samples.
- Texas (county view)
- USA (state view)
- USA (county view)
- Global (country view)
- Global (state view)
- Global (county view)
You can find the config files that runs this build in here.
To replicate this run, you need to first (1) install Nextstrain components and (2) download the ncov workflow. Please visit this page if you need more instruction on installation.
Once you can run a basic build of the ncov repository, clone this repository into the ncov folder. To run locally (without any advanced cluster submission), you could type:
nextstrain build . --configfile deltaInGreaterHoustonArea/builds.yaml