Get bulk ftp links from ENA

Question

[blackadder]

Hello everybody,

I hope you are doing well.

I need some help... I am trying to get ftp links for a big number of ENA assemblies.

What I have is a list with assembly accessions (I think that's the name) like:

GCA_021702275.1, GCA_014937245.1, GCA_021544875.1, ...

What I do now is to copy these accessions in the ENA browser text search and from there I can find the WGS Set Fasta link.

I found the ENA Advanced search tool, and the ENA API search but I was not able to figure how to get the ftp link.

Is there any way to automate this task?

Thanking you in advance!

[GenoMax]

Use https://sra-explorer.info/ to get this information.

See a tutorial here: sra-explorer : find SRA and FastQ download URLs in a couple of clicks

[blackadder]

Hello,

Thx for the reply.

I know this tool, is super helpful but it does not work with assembly accessions. I tried feeding it what i have and Im not getting any response. Or maybe I am missing something?

[GenoMax]

See answer below.

Answer 1

[GenoMax]

These are NCBI GenBank assembly accession numbers. You will want to use

NCBI datasets tool: https://www.ncbi.nlm.nih.gov/datasets/docs/v1/download-and-install/

[blackadder]

Hello,

Thank you for your help! The NCBI datasets tool i think its the solutions to my problem!

Thank you!!!