how to download data from COVID-19 Data Portal

Question

[2001linana]

I was trying to download data following the link https://www.covid19dataportal.org/sequences?db=embl-covid19. Here is what I did. So, I was interested in all the possible genome sequences, and I click the Sequences(27,649) button from the left panel. And then click the empty box in the first row (Accession, Collection Date, Country, Host, Strain, Isolate, Location, Mol. type, Taxonomy) of the table, to select all these sequences. And then click Download selected, and choose FASTA. The file I get is like of size 457KB. I was wondering, is this the correct way to download all the genome sequences ？

[GenoMax]

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Answer 1

[vmicrobio]

Hello,

I would use esearch:

esearch -db nucleotide \
        -query "txid2697049 [Organism] \
                AND (complete genome[Title] OR complete chromosome[Title]) \
                AND (contig[Title] OR plasmid[Title])" \
        | efilter -source insd \
        | efetch -format fasta \
        > GenomesCovid.fasta;