EagleView - The MarthLab

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1 Overview
2 Software Download
3 Sample and Test Datasets
4 Contacts

[edit] Overview

EagleView is an information-rich genome assembler viewer with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism candidate sites (e.g., SNPs) reported by polymorphism discovery tools. It can also facilitate data interpretation and hypothesis generation. EagleView is a multi-platform application developed with C++ and is available for all three major platforms: Windows, Linux, and Mac. For more details, please see EagleView publication at EagleView: a genome assembly viewer for next-generation sequencing technologies, Genome Res.,June 11, 2008

EagleView reads multiple data files including the standard ACE genome assembly file and optional READS, EGL, and MAP files. These optional files contain additional information of a genome assembly and can be visualized on EagleView. EagleView was designed with user's needs in mind. All these files are in simple text formats, which make it easy for creating customized data files and visualizing user-defined features on EagleView. The detail format for each type file is described in EagleView documentation. When EagleView opens an ACE file, it will automatically detect and load the associated optional files in the same directory.

Key Features

fast and memory efficient
pin-point view of machine-specific signals pin-point view of base quality
pin-point view of read id and strand distinct mark for discrepancy sites
genome annotation integration
navigation by read id and contig id
navigation by genomic features or user defined locations
navigation by both unpadded and padded positions
data utility tools included
zooming and printing capability
customizable font and color for viewer

[edit] Software Download

EagleView is distributed separately for different platforms. Each distribution contains everything including the core EagleView software, three utility tools for data preparation, and detailed documentation. The old beta version is still available here.

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[edit] MS Windows (XP or Vista) Distribution

Package: A single binary installer for either 32 or 64-bit system.

Installation: Double click EagleView installer and simply follow its instructions.

Launch: EagleView can launch from either Windows program menu or its shortcut at your Desktop

Download links:

EagleView-2.2-Setup-Win32.exe (32-bit)

EagleView-2.2-Setup-Win64.exe (64-bit)

[edit] Linux Distribution

Package: EagleView is distributed as a single RPM or Debian installation package for both 32-bit and 64-bit Linux systems. RPM packages are available for Fedora Linux (5 or above), Suse Linux (10.2 or above), and Redhat Enterprise Linux (4 or above) platforms. Debian package are available for Debian (4.0 or above) and Ubuntu Linux (7.04 or above). Installation: You need to be the root or a sudo user to install EagleView RPM or Debian package. RPM package Installation is done by issuing one line command at a terminal window:

        sudo rpm -i EagleView-ver.<platform>.rpm

For Upgrade

        sudo rpm -U EagleView-ver.<platform>.rpm

Debian package Installation is done by issuing one line command at a terminal window:

         dpkg -i EagleView-ver.<platform>.deb

Launch: issue the following command at your Linux terminal window:

       eagleview

Download links:

EagleView_2.2_CentOS5_x64_64.tar.gz EagleView tar package for 64-bit CentOS 5 or Redhat Linux 5

EagleView_Linux32.tar.gz(32-bit Linux tar package for Fedora, Suse, and Ubuntu Linux)

EagleView_Linux64.tar.gz(64-bit Linux tar package for Fedora, Suse, and Ubuntu Linux)

EagleView-2.2-0.i386.redhat.rpm(Redhat Enterprise Linux 32-bit)

EagleView-2.2-0.x86_64.redhat.rpm(Redhat Enterprise Linux 64-bit)

EagleView-2.1-0.i386.fedora.rpm(Fedora 32-bit)

EagleView-2.1-0.x86_64.fedora.rpm(Fedora 64-bit)

EagleView-2.1-0.i586.suse.rpm(Suse 32-bit)

EagleView-2.1-0.x86_64.suse.rpm(Suse 64-bit)

eagleview.2.1.i686.ubuntu.deb(Ubuntu Linux 32-bit)

eagleview.2.1.x86_64.ubuntu.deb(Ubuntu Linux 64-bit)

eagleview.2.1.i686.debian.deb (Debian Linux 32-bit)

[edit] Mac (OS X 10.4 or later with Intel CPU) Distribution

Package: A disk image contains Mac OS X installation Package

Installation: You need to have the administrator privileges to install EagleView. Installation is done by double clicking EagleView Installer EagleView_1.5_MacOS_X in the disk image

Launch: double click EagleView application at /Applications/eagleview. The data tools for EagleView should be used in the terminal window.

Download links:

EagleView-2.0.MAC_Installer.dmg (MacOS X with Intel CPU)