A Swiss army knife for genome projects
Latest commit 06d26fb Aug 13, 2013 @michaelbarton Merge branch 'release/0.1.0' closes #4
  * Genomer compatible with ruby 2.0.0 thanks to @robsyme
  * Use more secure https:// in genomer project Gemfile
  * Update all gem versions
  * Fix error where features were run from installed version
    of genomer rather than the version being developed.


Genomer: A swiss army knife for genome projects


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 and revision control tools such as git. This allows for all steps taken in genome project to be tracked and reverted if required.

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.


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 and for a larger microbial genome. Each of these projects takes advantage of revision control and build files to make the projects reproducible.



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

$ gem install genomer


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.


Genomer specifically requires the 1.2.x version of md2man. This is because later versions are not compatible with ruby 1.8.7 and I aim to keep genomer backwards compatible for as long as possible. If you find that there are errors running or developing genomer related to md2man please remove all versions from the systems and try reinstalling genomer. If you have further problems please contact the genomer mailing list found at the http://next.gs site.


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 used under a Creative Commons Attribution Non-Commercial ShareAlike 2.0 Licence. The original can be found on flickr.