Hi, I was trying to download SARS-CoV-2 sequences data from NCBI following this link: https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=SARS-CoV-2,%20taxid:2697049 When I click the empty box, I can only get like 200 sequences, each time. So I was wondering, is there a way to batch download all the genome sequences data with a click? Many thanks. I thought I did this earlier, but I do not quite recall.
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2001linana •
You can use NCBI Datasets for this. A dedicated page for Coronavirus Datasets is available. If you would prefer, a command line tool is also available. For example, you can use the command line tool to download SARS-Cov2 data as shown below:
datasets download virus genome taxon sars-cov-2 --complete-only --filename virus.zip
It looks like NCBI has 12 genomes of the original SARS virus (SARS total minus SARS-CoV-2). Can those be separately categorized in a link on the genome page?
Update: If I change the setting to All hosts from human it now shows 30246 SARS genomes but no SARS-CoV-2. Something does not seem right.
I click the empty box, I can only get like 200 sequences, each time.
Try this. Do not click any boxes. Click on Download button at top. In step 2 Download All Records should be automatically selected. This downloads ALL sequences. As of today that number stands at 43676 genomes (~1.2 GB file).
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You can get the assembly ids, and download from the ftp, for example:
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/
Many thanks for your kind reply. Could you be a bit more specific then? Many thanks.
I clicked on the link you posted, clicked on the tab for
Refseq Genome, clicked on the assembly:https://www.ncbi.nlm.nih.gov/assembly/GCF_009858895.2
Then clicked on
FTP directory for GenBank assemblyYou can get the fasta sequence by clicking on
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.fna.gz
And gene informations (gff format):
https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.gff.gz
I have downloaded those sequences, as you mentioned in march 2021; currently I am trying to download them again though I have faced errors and the download has failed any time I tried. I checked the NCBI command line, ENTREZ and viral datasets too, Do you have any other solution or Do you know any other available resource for SARS CoV 2 nucleotide and amino acid sequences?
I am downloading it now using
datasets download genome taxon sars-cov-2 --filename virus.zipwithout any issues. There are close to 340,000 genomes for SARS as of today.Edit: The final file was 8.8 G.