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.
| fast and memory efficient | genome annotation integration |
| 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 |
| navigation by read id and contig id | data utility tools included |
| navigation by genomic features or user defined locations | zooming and printing capability |
| navigation by both unpadded and padded positions | customizable font and color for viewer |
EagleView software is available through both its Academic and Commercial Licenses. The Academic License is for users from not-for-profit organizations and is free. The Commercial License is available for everyone. EalgeView software is distributed as binary installation packages currently available for Microsoft Windows (XP and Vista), a variety of Linux distributions, and Apple Mac OS X with Intel process. The current version is 2.1.
To request software, please fill and submit the following on-line registration form
Click here to register for academic users
For registered academic users, you can download software at the following link
Click here to download software for academic users
Note: You should receive a confirmation email within one hour (typically within 5 minutes) after your successful registration. If not, please register again or please send me an email.
EagleView should be cited as
Weichun Huang and Gabor T Marth, EagleView: a genome assembly viewer for next-generation sequencing technologies, Genome Res.,June 11, 2008, 10.1101/gr.076067.108
Important note: if your download file ends with suffix such as ".zip" or ".tar" (a problem with the firefox browser), please rename your download file by removing such a suffix. The valid filename extension of your download file should be: *.exe for Windows, *.rpm or *.deb for Linux, and *.dmg for MacOS X.
Package: A single binary installer for either 32 or 64-bit system (XP or Vista).
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
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 (8 or above), Suse Linux (10.2 or above), and Redhat Enterprise Linux (4 or above) platforms. Debian packages 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 -ih EagleView-Version.<platform>.rpmDebian package Installation is done by issuing one line command at a terminal window:
dpkg -i EagleView-Version.<platform>.debLaunch: issue the following command at your Linux terminal window:
eagleview
Package: EagleView Mac version is available for Mac OS X 10.4 or later with Intel CPU. The distribution is a disk image containing Mac OS X installation Package
Installation: You need to have the administrator privileges to install EagleView. Installation is done by double clicking EagleView Installer the disk image
Launch: double click EagleView application at /Applications/eagleview. The data tools for EagleView should be used in the terminal window.
Small example datasets
EagleView MAP files for Human genome annotation and SNP data
dbSNP SNP MAP files (chr1-chr10)[72MB]
dbSNP SNP MAP files (chr11-chrY)[45MB]
HapMap SNP MAP file (CEU population)[36MB]
HapMap SNP MAP file (CHB population)[36MB]
HapMap SNP MAP file (JPT population)[36MB]
HapMap SNP MAP file (YRI population)[36MB]
Datasets for efficiency tests
an e.coli K12 assembly of 6,822,388 Illumina reads [199MB]
a c.elegan chromosome II assembly of 14,562,818 Illumina reads [437MB]
a c.elegan chromosome V assembly of 19,566,095 Illumina reads [587MB]
Copyright© 2007-2008 Weichun Huang
