Hi, Molly! Please write us an email at info ncbi. Skip to content Given the size of modern sequence databases, finding the complete genome sequence for a bacterium among the many other partial sequences can be a challenge. Procedure 1. Example For this example our goal will be to explore the genome data available for Corynebacterium efficiens. Like this: Like Loading Leave a Reply Cancel reply.
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Project links Homepage. Maintainers kblin secmet. So this is a set of scripts that focuses on the actual genome downloading. Installation pip install ncbi-genome-download Alternatively, clone this repository from GitHub, then run in a python virtual environment pip install. If this fails on older versions of Python, try updating your pip tool first: pip install --upgrade pip and then rerun the ncbi-genome-download install.
Usage To download all bacterial RefSeq genomes in GenBank format from NCBI, run the following: ncbi-genome-download bacteria Downloading multiple groups is also possible: ncbi-genome-download bacteria,viral Note : To see all available groups, see ncbi-genome-download --help , or simply use all to check all groups. You can also use this with a slight trick to download genomes of a certain species as well: ncbi-genome-download --genera "Streptomyces coelicolor" bacteria Note : The quotes are important.
Multiple genera is also possible: ncbi-genome-download --genera "Streptomyces coelicolor,Escherichia coli" bacteria You can also put genus names into a file, one organism per line, e. This can be handy if you need to match a value in the middle of the NCBI organism name, like so: ncbi-genome-download --genera coelicolor --fuzzy-genus bacteria Note : The above command will download all bacterial genomes containing "coelicolor" anywhere in their organism name from RefSeq.
There is a "dry-run" option to show which accessions would be downloaded, given your filters: ncbi-genome-download --dry-run bacteria If you want to filter for the "relation to type material" column of the assembly summary file, you can use the --type-materials option.
Multiple values can be given, separated by comma: ncbi-genome-download --type-materials type,reference By default, ncbi-genome-download caches the assembly summary files for the respective taxonomic groups for one day. To get an overview of all options, run ncbi-genome-download --help As a method You can also use it as a method call.
Project details Project links Homepage. Download files Download the file for your platform. Files for ncbi-genome-download, version 0. On first use, a small sqlite database will be created in your home directory by default change the location with the --database flag. You can update this database by using the --update flag. Note that if the database is not in your home directory, you must specify it with --database or a new database will be created in your home directory.
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Installation pip install ncbi-genome-download. Streptomyces Amycolatopsis. Releases 11 Release 0. Jun 18, Packages 0 No packages published. You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window.
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