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Yale SARS-CoV-2 Genome Surveillance Initiative

In collaboration with the Yale School of Public Health, Yale School of Medicine, Yale New Haven Health, Yale University Environmental Engineering, and the CT Department of Public Health, we are using genomic epidemiology to uncover hidden patterns of the COVID-19 outbreak in Connecticut, the Northeast, and across the United States. This repository contains all of our data, results, and code.

WARNING: These results should be considered as preliminary data

Sequence data

The directory consensus-genomes contains the consensus SARS-CoV-2 genomes that we sequenced on the MinION from Connecticut and New York from clinical and environmental samples.

The directory 'metadata' contains all of the associated information for each sequence.

Nextstrain

The directory auspice contains the json that was produced using augor from the nextstrain pipeline. These results can be visualized using auspice, accessing the link below:


Weekly Updates

Update 1: 2020.April.03

The directory update1 contains the data, interpretation, and visualization of 18 new SARS-CoV-2 genomes (out of 27 sequenced until its date of release).

Update 2: 2020.April.07

The directory update2 contains the data, interpretation, and visualization of 13 new SARS-CoV-2 genomes (out of 40 sequenced until its date of release).

Update 3: 2020.April.15

The directory update3 contains the data, interpretation, and visualization of 30 new SARS-CoV-2 genomes (out of 70 sequenced until its date of release).

Paper1: Coast-to-coast spread of SARS-CoV-2

The directory paper1 contains the data, results, and code for our recent manuscript submitted to medRxiv. The paper can be accessed using the following link:

Fauver, Petrone, Hodcroft, et al., 2020. Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology


Grubaugh Lab | Yale School of Public Health (YSPH) | https://grubaughlab.com/

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