Consensus sequences

All consensus sequences and raw reads will be deposited under BioProject ID PRJNA612578.

PC00101PMT192765EPI_ISL_4146482020-03-11San Diego county0607399.75253516.14
MG0987EPI_ISL_4164572020-03-18San Diego county0607399.59542465.6

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 v1.1 (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



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