For any questions or help completing this form, please contact: covidgenomicepi@ph.lacounty.gov.
Lab Name* must provide value
Lab Address* must provide value
Type of Lab Clinical/Diagnostic Lab Research Lab Other
CLIA Number:
Research lab with or without academic affiliations? with academic affiliations without academic affiliations
Please specify other lab type:
Lab Director - Name* must provide value
Lab Director - Phone Number* must provide value
Lab Director - Email* must provide value
Is your Lab Director your Laboratory's Point of Contact? Yes No
Lab Point of Contact - Name* must provide value
Lab Point of Contact - Phone Number* must provide value
Lab Point of Contact - Email Address* must provide value
Does your lab conduct whole genome sequencing? Yes
No
When did your lab start sequencing SARS-CoV-2 samples?
Today M-D-Y
Average # of Sequences per Week
Source of Samples (Check all that apply)* must provide value
Own samples from diagnostic tests
Samples received from other lab(s)
Samples received from research institution(s)
Other
Please specify samples received from other lab(s):* must provide value
Please specify samples received from research institution(s):* must provide value
Please specify other samples:
What samples are selected for sequencing?* must provide value
All positive specimens of appropriate quality
Sample of positive specimens (If yes, describe)
Sequencing offered as commercial service
Research study samples
Other (must specify)
Please specify the sample of positive specimens:* must provide value
Please specify other method samples are selected for sequencing:* must provide value
Sequencing Platform* must provide value
Illumina
Oxford Nanopore
Pacific Biosciences
Ion Torrent
Other (must specify)
Please specify the other sequencing platform:* must provide value
Sequencing Library Prep Methods* must provide value
Commercial all-inclusive reagent kits (example - Illumina COVIDSeq, NEBNext ARTIC, QIAseq DIRECT SARS-CoV-2, etc - must specify)
Standard protocol (such as ARTIC v3 or v4 - must specify)
Other (must specify)
Please specify the commercial all-inclusive reagent kits:* must provide value
Please specify the standard protocol:* must provide value
Please specify other sequencing lab methods:* must provide value
Besides SARS-CoV-2, does your laboratory perform sequencing or analyze sequence data other microbial pathogens?* must provide value
Yes No
Please specify:
Quality Control Metrics* must provide value
Minimum percent reference genome coverage
Minimum depth of coverage
Minimum assembly length (unambiguous)
Maximum number of Ns
Use of quality control analysis tools (such as VADR, etc)
Minimum percent reference genome coverage
* must provide value
Minimum depth of coverage
* must provide value
Minimum assembly length (unambiguous)
* must provide value
Maximum number of Ns
* must provide value
Use of quality control analysis tools (such as VADR, etc)* must provide value
Partial sequencing* must provide value
Yes No
Provide a web link or insert an attachment of your protocol
Web link Attachment
Please provide the web link for your protocol.
Please provide an attachment for your protocol.
Describe targets for sequencing
PCR-based Approach* must provide value
Yes No
Specify PCR Instruments used * must provide value
Reagent Kit Used* must provide value
Commercial kit - with mandatory fields to specify name and vendor and must upload protocol
Laboratory-developed - must upload protocol
Commerical Kit Name* must provide value
Commerical Kit Vendor* must provide value
Please upload protocol for the Commercial Kit* must provide value
Please upload protocol for Laboratory-developed Reagent* must provide value
Brief description of targets* must provide value
Analysis pipeline* must provide value
Commercial pipeline (cloud-based or local - must specify) Open-source pipeline (cloud-based or local - must specify)
Cloud based or Local Cloud Based Local
Please specify the Commercial pipeline:
* must provide value
Cloud based or Local Cloud Based Local
Please specify the open-source pipeline:* must provide value
Please provide the weblink to reference or code repository (Github, etc):* must provide value
Is your lab currently sending all lineage results to public health via electronic laboratory reporting (ELR)? Yes No
If not, what is the primary reason?
If not, have you set up an alternative reporting mechanism with CDPH or LACDPH? Yes No
Is your laboratory currently uploading sequence data to a public repository (GISAID, NCBI)? Yes No
If yes, select which repositories?
GISAID (assembly FASTAs)
GenBank (assembly FASTAs)
NCBI SRA (FASTQs or BAMs)
What is the earliest among the repositories did your laboratory submit to? GISAID (assembly FASTAs) GenBank (assembly FASTAs) NCBI SRA (FASTQs or BAMs)
How many days does it take available results to be uploaded to this repository?
If no, are you currently submitting raw sequence data files to CDPH? Yes No
Are you able to report sequence identifiers through ELR (e.g. GISAID accession or virus name)? Yes No
If no, are you able to submit patient identifying information and sequence identifiers by flat file? Yes No