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A tool kit for accessing NCBI's GenBank

Project Description

NCBI Tool Kit

A tool kit for downloading and curating collections of genomes retrieved from the National Center for Biotechology Information’s public database, GenBank.

Requires rsync. Tested only with rsync version 3.1.2 protocol version 31.


Using pip:

pip install ncbitk


git clone
python install

Regardless of which installation method you choose, I recommend using a virtual environment.

Basic Usage

Download all GenBank bacteria:

ncbitk [directory] --update

If you have already run NCBITK, the above will also update your local collection, i.e. remove old genomes no longer in the assembly summary and download the latest assembly versions.

Get the status of your collection:

ncbitk [directory] --status

This will tell you how many genomes you have, what is missing from your collection, and how many deprecated genomes are present.

Release History

This version
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Source May 19, 2017

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