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kblin / ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers
Apache License 2.0
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Question about mitochondrial genomes #100

Closed ucbtmae closed 2 years ago

ucbtmae commented 4 years ago

Hello!

Congratulations on developing this neat solution to work with the new FTP directory. It's a time and lifesaver!

I wanted to ask if there is a way to batch download only complete mitochondrial genomes? I am going to be developing some new primers for metabarcoding, so it would be handy to see if the script can be tweaked to do it.

I already read the way to specify the download for other groups such as vertebrates or plants, so I think that is fine for the moment.

Thanks in advance!

kblin commented 4 years ago

I'm afraid the NCBI doesn't make mitochondria available separately at https://ftp.ncbi.nih.gov/genomes/refseq/

That said, you cam download all mitochondria at https://ftp.ncbi.nlm.nih.gov/refseq/release/mitochondrion/ and might be able to find an file describing if they are complete or not.

npsonis commented 2 years ago

Hi, currently mitochondria are available in https://ftp.ncbi.nih.gov/genomes/refseq/. Any chance to included it as an option? The same for plasmid, plastid...