cloe.SourceForge.net

CLOE

Cloe is open-source Java software for genome science. Cloe is a data visualization and manipulation tool for the finishing stage of DNA sequencing projects. The name Cloe stands for Closure Editor.

Project Overview

This is software for the whole-genome shotgun method of sequencing DNA: randomly selected fragments of sheared DNA are cloned in libraries characterized by fragment size; both ends of each fragment are sequenced by Sanger chemistry with an instrument such as the ABI 3730; fragment reads are computationally re-assembled with software such as the Celera Assembler; gaps in the assembly are closed by manual inspection, directed re-sequencing, and regional re-assembly; finished sequence is fed to software or teams of experts for annotation that reveals the encoded gene content.

Cloe is software for the finishing stage, also known as closure. This software allows a human editor to examine a draft assembly, to inspect multiple sequence alignments, to drill down to chromatograms (electropherograms), to edit base calls and alignments, and to order re-assembly. This software was developed at TIGR where it contributed to the sequencing and publication of hundreds of microbial genomes.

Written in Java, this software can run on many operating systems. This software expects the assembly is stored in a relational database.

Developer Resources

The PROJECT PAGE on Source Forge.
The source code under SVN VERSION CONTROL.
The SourceForge DATABASE of bug reports and feature requests.
Some SCREEN SHOTS.

This software was developed at The Institute for Genomic Research (TIGR) with financial assistance from the Microbial Sequencing Centers (MSC), part of the National Institute of Allergy and Infectious Disease (NIAID) at the National Insitutes of Health (NIH). The source is hosted by SourceForge.