MPI für molekulare Genetik / Department of Computational Molecular Biology |
|Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.|
|Authors:||Ye, Kai; Schulz, Marcel H.; Long, Quan; Apweiler, Rolf; Ning, Zemin|
|Date of Publication (YYYY-MM-DD):||2009-06-26|
|Title of Journal:||Bioinformatics|
|Issue / Number:||21|
|Full name of Issue-Editor(s):||Valencia, Alfonso|
|Copyright:||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.
|Review Status:||not specified|
|Abstract / Description:||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.
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.
|Comment of the Author/Creator:||To whom correspondence should be addressed. Kai Ye
Contact: firstname.lastname@example.org; email@example.com
Availability: The binary code and a short user manual can be freely downloaded from http://www.ebi.ac.uk/~kye/pindel/.
|External Publication Status:||published|
|Communicated by:||Martin Vingron|
|Affiliations:||MPI für molekulare Genetik|
|External Affiliations:||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.The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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