A simple genome scaffolder API for merging sequence contigs to build a continuous draft sequence. The draft sequence is constructed through specifying the order of contigs in in human-readable YAML files. Since the draft genome is specified by the scaffold YAML it is easy to remove or manipulate already sequences. In addition as the scaffold file is easy to edit and is ideal for version control and repeatability.

Feature List

  • Construct a draft sequence scaffold using human-readable and versionable plain text files.

  • A simple and extensible Ruby API to traverse the scaffold.


Ruby and RubyGems are required to use scaffolder. Scaffolder is compatible with at least Ruby versions 1.8.7 and 1.9.2. The last stable version of the RubyGems package manager is recommended for installing scaffolder.

Scaffolder is installed on the command line using:

$ gem install scaffolder


See the Scaffolder class for getting started with Scaffolder.


Scaffolder was developed by Michael Barton ( The website for scaffolder is at and a twitter feed for updates is available. There is a Google group for questions and comments. The source code is available on github. Bug reports and feature requests may also be made there.

Scaffolder © 2010 by Michael Barton. Scaffolder is licensed under the MIT license. Please see the LICENSE document for more information.