![Genomer: A swiss army knife for genome projects](http://genomer.s3.amazonaws.com/icon/genomer/genomer.png)

## About

Genomer is command line glue for genome projects. I wrote this tool to simplify
the small but tedious tasks required when finishing a genome. Genomer does not
perform assembly, gap closing or genome annotation. Genomer does however make
it easy to reorganise contigs in a genome, map annotations on to the genome and
generate the files required to submit a genome.

A important part of genomer is making all projects reproducible. Genomer is
designed to work well with build tools such as [GNU Make][make] and revision
control tools such as [git][git]. This allows for all steps taken in genome
project to be tracked and reverted if required.

[make]: http://www.gnu.org/software/make/
[git]: http://git-scm.com/

Genomer is also built as a modular tool where additional functions are added by
installing plugins. Plugins can be added simply by naming them in the `Gemfile`
in the genomer project root, followed typing the command `bundle install`.
Furthermore plugins can be specified to specific versions, this means that new
versions of genomer plugins will not break any existing genomer projects.

## Examples

I wrote genomer to simplify the manual and error prone tasks in my own genome
projects. You can see examples of using genomer for [a small plasmid][plasmid]
and for [a larger microbial genome][genome]. Each of these projects takes
advantage of revision control and build files to make the projects
reproducible.

[plasmid]: https://github.com/michaelbarton/chromosome-pfluorescens-r124-plasmid
[genome]: https://github.com/michaelbarton/chromosome-pfluorescens-r124-genome

## Screencasts

  * [Installing Genomer](http://www.youtube.com/watch?v=bXws8RnBsUU)
  * [Genomer example usage](http://www.youtube.com/watch?v=HfsdJOELFjs)
  * [Generating Genbank upload files for a simple plasmid](http://www.youtube.com/watch?v=jVn62pMnIRA)

## Installing

Ruby and RubyGems are required to use genomer and related plugins. Genomer is
installed on the command line using:

    $ gem install genomer

## Contact

Genomer is developed by Michael Barton (www.michaelbarton.me.uk). The source
code is available on [github][]. Bug reports and feature requests should also
be made there.

[github]: https://github.com/michaelbarton/genomer

## Copyright

Genomer copyright (c) 2010 by Michael Barton. Genomer is licensed under the MIT
license. See LICENSE.txt for further details. The swiss army knife image is by
[Alan Cann][cann] used under a Creative Commons Attribution Non-Commercial
ShareAlike 2.0 Licence. The original can be [found on flickr.][flickr]

[cann]: http://microbiologybytes.com/AJC/
[flickr]: http://www.flickr.com/photos/ajc1/4663140532/