Download genome complete referenc with Taxid or Name with comand line
Hi,
How could I download by command line, a reference genomes with name or taxid, as *.fna file from https://www.ncbi.nlm.nih.gov/datasets/genomes/ assembly level complete or chromosome?
I want to build a kraken2 db automatically.
Thanks
1 answer
Use genome_updater: https://github.com/pirovc/genome_updater.
NCBI datasets should also work: https://www.ncbi.nlm.nih.gov/datasets/docs/v1/download-and-install/
Log in to answer this question.
More posts like this
-
some error in building kraken2 database
written by Art1ess •
-
kraken2 database error: `No preliminary seqid/taxid mapping files found, aborting.`
written by 10mz1 •
-
kraken2-build not finish
written by spatroca •
-
Adding new taxa to a Kraken2 db
written by valentinavan •
-
fail to build kraken2 database (custom and standard)
written by ramin.k2013 •
-
kraken2-build and kraken-build both return error on viral db
written by emiliomastriani •
-
Assembly not in scope for NCBI Datasets
written by Valentin •
-
How much time should be expected for building a database by kraken2-build?
written by thitrucminh.nguyen •
-
more elegant way to bulk download genomes from the NCBI
written by Carambakaracho
-
How to download COMPLETE bacterial genomes from NCBI based on list of names?
written by taojincs •
