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Bioinformatics Advance Access originally published online on June 26, 2009
Bioinformatics 2009 25(21):2865-2871; doi:10.1093/bioinformatics/btp394
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

Kai Ye 1,2,*, Marcel H. Schulz 1,3, Quan Long 4, Rolf Apweiler 1 and Zemin Ning 4,*

1 EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, 2 Departments of Molecular Epidemiology, Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands, 3 Max Planck Institute for Molecular Genetics and International Max Planck Research School for Computational Biology and Scientific Computing, Berlin, Germany and 4 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

* To whom correspondence should be addressed.


  Abstract

Motivation: There is a strong demand in the genomic community to develop effective algorithms to reliably identify genomic variants. Indel detection using next-gen data is difficult and identification of long structural variations is extremely challenging.

Results: We present Pindel, a pattern growth approach, to detect breakpoints of large deletions and medium-sized insertions from paired-end short reads. We use both simulated reads and real data to demonstrate the efficiency of the computer program and accuracy of the results.

Availability: The binary code and a short user manual can be freely downloaded from http://www.ebi.ac.uk/~kye/pindel/.

Contact: k.ye{at}lumc.nl; zn1{at}sanger.ac.uk

Associate Editor: Alfonso Valencia

Received on April 27, 2009; revised on June 20, 2009; accepted on June 21, 2009

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