Repository to store the most up to date code to Wisconsin Nextstrain builds
This build serves to represent all sequences that our lab has generated, as well as sequences from around the state of Wisconsin.
This build directory contains 5 unique builds:
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ncov/wisconsin/global-context
This build serves to represent all WI sequences and to pull in sequences from around the globe to contextualize our findings.
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ncov/wisconsin/statewide
This build serves to represent all WI sequences on their own so we can see the relationship between counties.
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ncov/wisconsin/dane-county
This build serves to represent all Dane County sequences - where the University of Wisconsin - Madison is located. The vast majority of sequences that we generate are from Dane County.
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ncov/wisconsin/milwaukee-county
This build serves to represent all Milwaukee County sequences. This county is the largest and most populous in Wiscosin.
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ncov/wisconsin/avrl
This build serves to represent only the sequences that we have generated at AVRL.
Gage Moreno and Kat Braun performed viral RNA extractions, sample preparation for sequencing, performing and interpreting the phylogenetic analysis, and keeping our OpenResearch Portal up to date. David Baker manages our ARTIC pipeline. JJ Baczenas manages file organization and uploaded sequences to GISAID. Gage Moreno, Kat Braun, Dave O’Connor, and Thomas Friedrich maintain this Wisconsin build.
We gratefully acknowledge Dr. Trevor Bedford and the entire Nextstrain team for making Nextstrain phylogenetic tools publicly available and for their commitment to tracking the global spread of SARS-CoV-2. We also acknowledge the GISAID team for maintaining the largest public repository of SARS-CoV-2 sequence- and metadata. This project was funded in part through a COVID-19 Response grant from the Wisconsin Partnership Program at the University of Wisconsin School of Medicine and Public Health to TCF and DHO.