A script for updating a local directory with genomes, from NCBI assembly files
genome_update is a package that downloads genomes from NCBI and saves information about them in a yaml file. It can also use a local yaml file to update and download new genomes.
Sequence statistics is also calculated for each genome and added to the yaml file.
## Getting Started
These instructions will provide information how to install and use the software.
Python Pandas PyYaml
### How to install
To install Genome_update you can either download source code directly from github and build it your self, an easier alternative is to use pip.
Installing by pip:
` pip install genome_update ` Pip will also install all prerequisities. It is also recommended to update all prerequisities.
Installing genome_update and upgrading prerequisities:
` pip install genome_update --upgrade `
Download all genomes from a specific genus: ` genome_update -g <Genus> `
Download all genomes from a specific genus, but much faster: ` genome_update -g <Genus> -p <threads> `
Download all genomes from a specific genus, but much faster, to a specific directory (default is /genomes): ` genome_update -g <Genus> -p <threads> -o <directory> `
Download all genomes from a specific species: ` genome_update -g <Genus> -s <species_taxid> `
To update a local yaml file: ` genome_update -u -i <yamlfile> `
To download missing genomes from a local yaml file: ` genome_update -d -i <yamlfile> `
To download genomes from another domain than bacteria: ` genome_update -domain <domain> -g <Genus> `
- Emil Samuelsson - Initial work - [Emisam](https://github.com/Emisam)
This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details
- Would like to thank kblin for his amazing work with the ncbi_genome_download which provided lots of inspiration when writing genome_update.
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