1 Genome analysis VAGUE: a graphical user interface for the Velvet assembler

Summary: Velvet is a popular open-source de novo genome as-sembly software tool which is run from the Unix command line. Most of the problems experienced by new users of Velvet revolve around constructing syntactically and semantically correct command lines, getting input files into acceptable formats, and assessing the output. Here we present VAGUE (Velvet Assembler Graphical User Envi-ronment), a multi-platform graphical front-end for Velvet. VAGUE aims to make sequence assembly accessible to a wider audience, and to facilitate better usage amongst existing users of Velvet. Availability and Implementation: VAGUE is implemented in JRuby and targets the Java Virtual Machine. It is available under an open-source GPLv2 licence fro