Orchid Assembly Viewer

Orchid is a data analysis tool designed to view paired end relationships from assembled shotgun sequencing data. It reads the new ace file format from the phrap/Consed assembly suite and displays the assembly with subclones as parabolas and the contigs auto-ordered by links. Orchid also gives an indication of potential problem areas based on the size of the subclone links and can be customized to display annotation of the sequence and assembly in a ring style format. It is in use by many genomes centers as a QC and finishing tool.

The current version is 2.0.1. New features include:

Infinite zooming and new draw routines

Complete configuration from an orchidrc file

Hide junk contigs

The Orchid source tree is originally derived from Exgap, a program developed by Axin Hua at the University of Oklahoma Advanced Center for Genome Technology.