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I'm taking a genomics course at school, and we have a final project due in a few weeks. Now, I can write bash scripts to sort and analyze the data, etc. However, I'm not quite sure how to actually get the data from the database. I was hoping to get some help there.

I'd like to get the assemblies of genomes for the species in the Borrelia genus. Is there any way that I can do this using commands like "wget", for example. I'm not even sure what URL I'd have to give the computer to go fetch these. Then once I give it the correct URL, how should I tell it what file in that directory to download?

I'd greatly appreciate some help on this issue.

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  • $\begingroup$ Have you tried Google on something like Borrelia genome? I've never done it before but it took me less than 10 minutes to find the genome for a borrelia species from that point. $\endgroup$ – mgkrebbs Nov 7 '18 at 20:37
  • $\begingroup$ @mgkrebbs - I'm sorry, but I forgot to mention in my post, that I need the genomes for many species of Borrelia. I wanted to know that, instead of doing it manually, is there some way I could get the computer to download the assemblies for all the Borrelia species in Genbank? $\endgroup$ – The_Questioner Nov 7 '18 at 21:18
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    $\begingroup$ Entrez is what you want for this, most likely. There are R/python packages that can also access it pretty easily (biomaRt/biopython, respectively). $\endgroup$ – Jared Andrews Nov 7 '18 at 23:04
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    $\begingroup$ Do you need the assembly information and metadata? or do you need the genomes sequences themselves? $\endgroup$ – MikeKatz45 Nov 13 '18 at 16:48
  • $\begingroup$ @mgkrebbs Getting data off of NCBI is infuriatingly difficult and non-obvious, if you don’t know exactly what you’re looking for. Finding the data is one thing (already not quite as easy as you make it sound). And then …?! $\endgroup$ – Konrad Rudolph Dec 10 '18 at 17:45
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For downloading data from commandline use the E-utilities of NCBI.

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  • $\begingroup$ Can you edit your answer to provide an example query to download all of the Borrelia genomes from NCBI using the tool that you linked? $\endgroup$ – conchoecia Dec 10 '18 at 17:21
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    $\begingroup$ @conchoecia I answered this in Biology and therefore did not go into details. I'll provide an example as soon as I can. $\endgroup$ – WYSIWYG Dec 10 '18 at 19:19

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