Figaro

Figaro is a software tool for identifying and removing the vector from raw DNA sequence data without prior knowledge of the vector sequence. By statistically modeling short oligonucleotide frequencies within a set of reads, Figaro is able to determine which DNA words are most likely associated with vector sequence. For a description of Figaro's algorithms please see our [ http://bioinformatics.oxfordjournals.org/cgi/content/full/24/4/462 paper]. You may download Figaro individually, or as part of the AMOS package at Sourceforge.

Contributors.

• james robert white
• michael roberts
• mihai pop
• james yorke

Requirements

Figaro is released as C++ and Perl source code and should work on any Unix system. We strongly encourage users to quality trim their data as well using a program such as Lucy. Lucy can be downloaded here or at ftp://ftp.tigr.org/pub/software/Lucy/.

Documentation and Data

• Figaro User Manual - In depth description of how to run
• Figaro Simulated Data - Simulated data discussed in our paper.

Keywords.

vector trimmer, vector clipping, vector trimming, open source, AMOS.