Overview

Consensus sequences

All consensus sequences will be deposited on GISAID and on NCBI under BioProject ID PRJNA612578. metadata.csv contains collection dates, location, originating labs and sequencing metrics: coverage and average depth.

Location Number of sequences
Asia / Jordan / Amman 26
Asia / Jordan / Irbid 2
USA/California/San Diego 187
USA/Louisiana/New Orleans 117

Raw read files

Raw read files for both Illumina and Oxford Nanopore data are available on,

The sequencing is being performed using an amplicon-based sequencing scheme using PrimalSeq with artic nCoV-2019 scheme.

Nanopore data was processed using the artic-nCoV019 pipeline with minimap2 and medaka. Illumina data was processed using iVar (Grubaguh et al. Genome Biology 2019) with bwa.

Disclaimer. Please note that this data is still based on work in progress and should be considered preliminary. If you intend to include any of these data in publications, please let us know – otherwise please feel free to download and use without restrictions. We have shared this data with the hope that people will download and use it, as well as scrutinize it so we can improve our methods and analyses. Please contact us if you have any questions or comments – we’ll buy beers for #ResearchParasites that spot flaws and faults in the data and come up with improvements!


Andersen Lab
The Scripps Research Institute
La Jolla, CA, USA
data@andersen-lab.com

Phylogeny

Nextstrain Narratives

narrative

Narrative 1 | Genomic Epi in San Diego

| Data, Narrative | No Comments
To gain insights into the the emergence, spread, and transmission of COVID-19 in our community, we are working with a large number of partners to sequence SARS-CoV-2 samples from infected patients in San Diego. This is our first preliminary analysis. (more…)

People

Collaborators

San Diego Partners
SEARCH Alliance, San Diego

San Diego County Public Health Laboratory
Tracy Basler, Jovan Shephard, Brett Austin

UCSD – Center for Advanced Laboratory Medicine
Jenny Shin, David Pride

Rady Children Hospital, San Diego
Christina Clarke, Michelle Vanderpool, Teresa Mueller, Denise Malicki

Scripps Health, San Diego
Michael Quigley, Ellen Stefanski, Ian Mchardy

New Orleans
Allison Smither, Gilberto Sabino-Santos, Patricia Snarski, Lilia Melnik, Antoinette Bell, Kaylynn Genemaras, Arnaud Drouin, Dahlene Fusco, Robert Garry

Louisiana
Jeremy Kamil, Vaughn Cooper

Jordan
Issa Abu-Dayyeh, Ahmad Tibi, Lama Hussein, Lina Mohammad, Zein Naber, Amid Abdelnour

Analysis Partners
Marc Suchard, UCLA
Lauren Gardner, Johns Hopkins
Philippe Lemey, KU Leuven
Alexander Watts & Kamran Khan, BlueDot
Emma Hodcroft, Nextstrain

GitHub Commits

Data

Protocols

Funding

scripps research

NIAID