Question: how to download data from COVID-19 Data Portal
0
gravatar for 2001linana
16 days ago by
2001linana20
2001linana20 wrote:

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 ?

sequencing • 75 views
ADD COMMENTlink modified 16 days ago by vmicrobio260 • written 16 days ago by 2001linana20

2001linana : Please follow up on your past questions by upvoting comments/answers that help. Accept answers (green check mark) to provide closure to threads. People who participate on biostars volunteer their time for free so acknowledging their assistance is how you can show your appreciation.
Upvote|Bookmark|Accept

ADD REPLYlink written 15 days ago by GenoMax92k
1
gravatar for vmicrobio
16 days ago by
vmicrobio260
vmicrobio260 wrote:

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;
ADD COMMENTlink written 16 days ago by vmicrobio260
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2176 users visited in the last hour