%0 Journal Article
%T Scaffolder - software for manual genome scaffolding
%A Michael D Barton
%A Hazel A Barton
%J Source Code for Biology and Medicine
%D 2012
%I BioMed Central
%R 10.1186/1751-0473-7-4
%X The software outlined here, ˇ°Scaffolder,ˇ± is implemented in the Ruby programming language and can be installed via the RubyGems software management system. Genome scaffolds are defined using YAML - a data format which is both human and machine-readable. Command line binaries and extensive documentation are available.This software allows a genome build to be defined in terms of the constituent sequences using a relatively simple syntax. This syntax further allows unknown regions to be specified and additional sequence to be used to fill known gaps in the scaffold. Defining the genome construction in a file makes the scaffolding process reproducible and easier to edit compared with large FASTA nucleotide sequences.Scaffolder is easy-to-use genome scaffolding software which promotes reproducibility and continuous development in a genome project. Scaffolder can be found at http://next.gs webcite.
%U http://www.scfbm.org/content/7/1/4/abstract