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Bioinformatics. 2009 Nov 1;25(21):2865-71. doi: 10.1093/bioinformatics/btp394. Epub 2009 Jun 26.

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

Author information

  • 1EMBL Outstation European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. k.ye@lumc.nl

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/ approximately kye/pindel/.

CONTACT:

k.ye@lumc.nl; zn1@sanger.ac.uk.

PMID:
19561018
[PubMed - indexed for MEDLINE]
PMCID:
PMC2781750
Free PMC Article

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