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Bioinformatics Advance Access published online on January 6, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp011
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SCARF: Maximizing next-generation EST assemblies for evolutionary and population genomic analyses

Michael S. Barker 1,2,{dagger},*, Katrina M. Dlugosch 1,{dagger}, A. Chaitanya C. Reddy 1, Sarah N. Amyotte 1 and Loren H. Rieseberg 1,2

1Botany Department, University of British Columbia, Vancouver, B.C. V6T 1Z4, Canada
2Department of Biology and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA

*To whom correspondence should be addressed. Mr. Michael Barker, E-mail: msbarker{at}indiana.edu


  Abstract

Summary: SCARF is a next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high quality reference sequences from related species. The program was created to knit together low coverage 454 contigs that do not assemble during traditional de novo assembly, using a reference sequence library to orient the 454 sequences.

Availability: SCARF is freely available at http://msbarker.com/software.htm, and is released under the open source GPLv3 license (http://www.opensource.org/licenses/gpl-3.0.html).

Contact: msbarker{at}indiana.edu

Associate Editor: Dr. Joaquin Dopazo

{dagger}Co-first authors

Received on November 4, 2008; revised on December 18, 2008; accepted on January 1, 2009

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