Downloading unique data from refseq
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8.1 years ago

Hi

I would like to download all the bacterial files from the genome database bearing .fna.gz extension in one go. The problem is that there are around 10000 bacterial entries in the database and each filename is unique. Any suggestions.

fasta bacteria refseq • 1.8k views
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I would suggest that it would be a good idea to use the search.

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@avinashdhar123: When you use this method to download the data make a note that NCBI has moved the bacterial genomes to this directory: ftp://ftp.ncbi.nih.gov/genomes/refseq/bacteria/

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Thank you for the reply. Command I used is:

wget -cNrv -t 45 -A ".fna" "ftp://ftp.ncbi.nih.gov/genomes/refseq/bacteria/"

After running this command only folders are downloading not the files inside it.

Any suggestions.

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NCBI is not very easily organized now.

See the post C: where can I get environmental bacteria genome in fasta format (as many as possib,

and my answer inside it, it may help you.

ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Bacteria/

you will find the file you need in the list above. It is not updated,

recently sequenced bacteria are absent there.

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