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tgvaughan / R0-manuscript-materials

Supplemental files and data for the manuscript "Estimates of early outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data".
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how to use the file "extract_sequence_dates.sh", thanks. #1

Closed liamxg closed 8 months ago

liamxg commented 9 months ago

Dear @tgvaughan,

Very nice project, I want to know how to use the file "extract_sequence_dates.sh", thanks.

tgvaughan commented 8 months ago

Dear Liam, thanks for your interest! Both the extract_sequence_dates.sh script and the analyses themselves require sequences which have been procured from GISAID and which we are not allowed to further distribute. To acquire these sequences, you'll need to create a GISAID account. Accession numbers for these sequences can be found in the /sequences/ directory of this repository.

liamxg commented 8 months ago

Dear @tgvaughan, Thanks, could you tell me what kind of sequence name should we prepare, and what is the command for this, thanks.

tgvaughan commented 8 months ago

Hi Liam, I've added some more detailed instructions to a README.md in the sequences folder which should help.

If you like, feel free to get in touch with me directly (email in paper) and, provided you can show me proof of having personally accepted the GISAID distribution terms for the SARS-CoV-2 sequences (eg sending me your GISAID account creation confirmation email) , I can share the sequence files with you directly and shortcut a lot of hassle.