Hi!
I need to create and maintain an updated database of all complete and annotated SARS-CoV-2 genomes that I could find at NBCI.
I am pretty new to this, so I managed to get until the point where I can list all the entries by using the search querys of this link: https://www.ncbi.nlm.nih.gov/nuccore/?term=Severe+acute+respiratory+syndrome+coronavirus+2%5Borganism%5D+AND+complete
However, if I make the usual process of downloading it through "Send To>File>Format:GenBank (Full)", I end up with only one big .gb file (4.66MB instead of the regular ~50KB).
Is there any way I can download all those sequences as separate files (without having to download them individually), or separate this big .gb file into the individual entries?
Thanks!
Dear,
are you sure that you need the sequences on ".gb" format? Or you need the ".fasta" format? Anyway, you will need download all genomes in only one file and after you will separate then. After that you will need using a programming lenguage for separate the genomes in different files.
For separeate a ".fasta" file you may use this script: https://github.com/mmarchin/utilities/blob/master/all2many.pl, for separeate a ".gb" will be necessery create a script.
Please, if you don't know how use this tools (linux, programing...) and still are need help, contat with me, i may help you.
Hi,
Download multiple files in a fasta format from NCBI and then use them separately.
You can also see at this link:
https://www.youtube.com/watch?v=OC74-DpkWjE
Hi, Edson Mario de Andrade Silva
Yeah, I wish I could download them as .fasta, but they specifically requested me to download it as .gb. Nevertheless, that script seems very useful, I've downloaded it since I'm sure it'll come handy to me someday. Thanks!
Dilraj Kaur , I did not know the NCBI YouTube channel, thanks!
Pedro Abilleira
To download the ".fasta" format, you need to select the "FASTA" option, instead of "GenBank (Full)". So, the path would be: "Send To> File> Format: FASTA".
It will be easier for you to get the separate genome files, using the fasta format. Good luck!
Pedro Abilleira I hope it works. Also I post if I will get anything more regarding this.
First search the SARS-CoV-2 genomes on ncbi, highlight the data set that you wnat, click on fasta, then dowload
Thanks everyone..................Especially Pedro Abilleira Asemoloye Micheal Dare Dilraj Kaur Edson Mario de Andrade Silva
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