Figaro

Figaro is a software tool that identifies and removes vector sequences from raw sequence data without prior knowledge of the vector sequence. The vector sequence is inferred by analyzing the frequency of occurrence of short oligo-nucleotides using Poisson statistics. The tool achieves 99.98% sensitivity when tested on approximately 1.5 million shotgun reads from Drosophila pseudoobscura. Figaro is released under an open-source license through the AMOS package.

Topic

Sequencing

Detail

  • Operation: k-mer counting

  • Software interface: Command-line user interface

  • Language: C++;Perl

  • License: The Artistic License 2.0

  • Cost: Free

  • Version name: 3.1.0

  • Credit: National Institutes of Health (NIH), the Uniformed Services University of the Health Sciences administered by the Henry Jackson Foundation, NSF, University of Maryland NSF VIGRE fellowship.

  • Input: -

  • Output: -

  • Contact: Mihai Pop mpop@umiacs.umd.edu, James A Yorke Yorke@umd.edu

  • Collection: -

  • Maturity: Stable

Publications

  • Figaro: a novel statistical method for vector sequence removal.
  • White JR, et al. Figaro: a novel statistical method for vector sequence removal. Figaro: a novel statistical method for vector sequence removal. 2008; 24:462-7. doi: 10.1093/bioinformatics/btm632
  • https://doi.org/10.1093/bioinformatics/btm632
  • PMID: 18202027
  • PMC: PMC2725436

Download and documentation

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