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New 2013 Lucy2 Release!

We are glad to release a complete reimplementation of the Lucy2 software to the public. This new version contains the following features:

  • Re-implementation of the Graphic User Interface for Lucy, based on the code-base of lucy 1.20. This version contains all functionality of lucy 1.20
  • The ability to read from and write to FASTQ data formats
  • An improved multi-threading computation capability different from the lucy 1.20 pthread models
  • The ability to independently open and process multiple input files in any order
  • True cross-platform deployment for Windows, Mac and Linux, including both 32-bit and 64-bit versions (on the Mac it's a single FAT application)
  • A new color scheme for sequence quality and trimming result representations
  • Improved parameter setting dialogs, use-helps, error-corrections and configuration saving across sessions
  • Overall stability and input data file compatibility improvements.

You need to register again to download this new version. For bug reports and suggestions, please email to We hope you will like this new version!


Most of the bioinformatic tools operating on DNA data assume that the sequences are trustworthy. However, raw data obtained from sequencing machines often violate this assumption. The tool Lucy1 was previously created to solve the raw data quality assurance problem.

Lucy2 is a raw DNA sequence trimming and visualization tool based on the command-line tool Lucy1. Lucy1 was originally designed for high-throughput DNA sequencing centers to easily "plug-in" to their data streams; therefore it is operated exclusively through a command-line syntax. This style of operation was not suitable to individuals who may just like to trim a few sequences since it is inconvenient for users to operate with Lucy1 command-line syntax and to memorize its parameters. With Lucy2, these users can perform Lucy1's functionality through a much friendlier user interface. In addition, Lucy2 gives the option for users to physically remove the bad region before saving the data.

Lucy2 is an open source project. The binary executable files are currently available on Windows, Linux and MacOS.

How to Download Lucy2

  1. Input your email into the box at the bottom of Registration section.
  2. Press "Enter" on your keyboard. You should be taken to a confirmation screen.
  3. Check your email. Your should get an email from us with a password.
  4. Go to the Download page and input your username and password. Your username is the email you registered with and the password is the one you got in email.
  5. Click on "Submit" and you should be taken to the download page where you can download Lucy2.


Please register your email address with us to obtain your download password. This is necessary for several reasons:

  1. We can send you email notices when newer versions of Lucy2 become available;
  2. We can provide our grant agency anonymous usage statistics of our software. This helps keep us in business so we can continue to improve Lucy2 to serve you better; and
  3. We filter all incoming inquiry emails against our registration list to prevent spams. Therefore if you would like to send us a question in email, you need to register. Otherwise, we will not recieve your email inquiry.

Your email address will only be used for this purpose. If you have forgotten your password, you can retrieve it by entering your email again. Your password will be automatically emailed to you shortly, then you can go to our download page to download Lucy2.

Please input your email address and then press return:

Your email address:


For users interested in Lucy1 for their unattended sequence trimming, it can be downloaded directly from SourceForge.

A tutorial was developed to help users better understand Lucy2. This tutorial introduce the features of Lucy2 and better aquaint the user with its functionality and interface. Users can quickly gain first hand experience of Lucy2 and begin data cutting after completion of these tutorials:

Lucy2 Guided Tour
: Acquaints users with a thorough explanation of Lucy2 user interface and functionality. [Download PDF Version]

Related Papers

1. LUCY2: an interactive DNA sequence quality trimming and vector removal tool

Bioinformatics Advance Access published on May 6, 2004
Song Li and Hui-Hsien Chou Bioinformatics, Nov 2004; 20: 2865-2866.

2. DNA sequence quality trimming and vector removal
Hui-Hsien Chou and Michael H. Holmes.Bioinformatics. 2001. 17(12):1093-1104.

Last modified June 13, 2008 . All rights reserved.

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