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How to download coronavirus genomes and its metadata file in only animals

Hi, I am trying to download all coronavirus complete genomes in only animals and its metadata (including countries, releasing date, accession number etc) from NCBI. Please suggest any methods or scripts to download it.

coronavirus ncbi metadata genome
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updated by MirianT_NCBI • MirianT_NCBI • written by Kumar Kumar

2 answers

Thank you for your reply.

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written by Kumar Kumar

Hi,
you can use NCBI datasets. The default data package includes the genomic sequences in FASTA format, and a metadata file in JSON-Lines. Here's how to download all complete coronavirus (I'm assuming SARS-COV-2 here) using the command line tool.

datasets download virus genome taxon sars-cov-2 --complete-only

The data report included has all this information you want. You can use dataformat, which is a datasets companion tool.

Please let me know if this is what you're looking for, or feel free to ask additional questions :) Thanks! Mirian

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written by MirianT_NCBI • MirianT_NCBI

MirianT_NCBI OP wants non-human corona virus sequences. Your solution above seems to download all sars-cov-2 genomes, is that correct?

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written by GenoMax GenoMax

You are correct GenoMax . I completely misinterpreted the question (animals = Metazoa). In that case, OP could download a list of accessions from the NCBI Virus website and use as input to the command datasets download virus genome accession --inputfile sequences.acc, if that makes sense for them (if they want to download everything directly to a server for example).

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written by MirianT_NCBI • MirianT_NCBI

Thank you for your reply. Yes, as GenoMax replying, I am looking to download only non-human.

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written by Kumar Kumar

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