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Question: Retrieve multiple refseq genomes in seperate fasta files
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gravatar for Biogeek
8 months ago by
Biogeek • 400
Biogeek • 400 wrote:

I've had a search and I can't seem to find any relatable questions.

My task is as follows:

  1. I have a list of Refseq accessions in a .txt file.
  2. I want to download all the associated genomes to seperate .fasta files in a local directory.

I note that I can use Entrez or NCBI assembly downloader, but this puts all genomes into the one .fasta file which isn't ideal.

Can anyone help?

Thanks.
refseq genome download ncbi • 148 views
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written 8 months ago by Biogeek • 400
1
gravatar for GenoMax
8 months ago by
GenoMax ♦ 96k
United States
GenoMax ♦ 96k wrote:

I note that I can use Entrez or NCBI assembly downloader, but this puts all genomes into the one .fasta file which isn't ideal.

How about using a loop and multiple calls to the said programs. That should give you separate files.
ADD COMMENT • link written 8 months ago by GenoMax ♦ 96k

Good call genomax, thanks! I've now installed the Entrez utilities and can obtain my record with efetch. I'll write a loop using the 'list.txt' file I have which contains accession numbers.

One more question, apologies for the ignorance (as required), is there a way I can also obtain my .fasta files with the TaxId on the headers as well?

Thanks!

ADD REPLY • link written 8 months ago by Biogeek • 400

If you use Entrezdirect then use epost method instead of a loop. It will do the same thing. You will need to post-process the files to add taxID to headers. I don't think there is a way to do this automatically.

ADD REPLY • link written 8 months ago by GenoMax ♦ 96k
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