Set of tools for manipulating sequence assemblies specified by yaml configuration files.
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A command line tool for processing genome scaffolds defined by the genome scaffolder API.

Feature List

  • Output scaffold to fasta format.

  • Test inserts do not overlap in the scaffold.


Ruby and RubyGems are required to use scaffolder. Scaffolder tools is installed on the command line using:

$ gem install scaffolder-tools


Command line usage can be found by running the following:

$ scaffolder help

A unix man page is available for each scaffolder command by typing:

$ scaffolder help COMMAND


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.