Pindel: A Pattern Growth Approach to Detect Break Points of Large Deletions and Medium Sized Insertions From Paired-End Short Reads

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

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Chromosome Breakpoints*
  • Computational Biology / methods*
  • DNA Breaks
  • Genome
  • INDEL Mutation*
  • Sequence Analysis, DNA
  • Software*