I am working on a project that requires me to download all 120 available turtle genome fasta files from NCBI. I am unsure about the most logical and efficient way to do this. Should I use the entrez e-utilities or the datasets utility?
Any example code would be helpful.
Thanks in advance.
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skibstedm •
NCBI datasets is the way to go for this: https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/download-genome/
Use:
$ datasets download genome accession ACCESSION_NUMBER--filename accession_dataset.zip
You can get the accession numbers from the tables here (if you don'r already have them) : https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=8464 and https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=8460
Hi!
Another option would be to download the genomes using the taxon option.
datasets download genome taxon testudines --filename testudines.zip
Let me know if you have any other questions.
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