Difference between revisions of "Figaro"
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| − | 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 | + | 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 [http://sourceforge.net/project/showfiles.php?group_id=134326 AMOS package at SourceForge]. |
Latest revision as of 17:35, 28 October 2009
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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 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.
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.
