Pindel

Pindel is a computer program that uses a pattern growth approach to detect breakpoints of large deletions and medium-sized insertions from paired-end short reads. The tool is able to accurately detect indels and long structural variations using both simulated reads and real data. Pindel is freely available for download and comes with a short user manual.

Topic

DNA structural variation

Detail

  • Operation: Localised reassembly;Read mapping;Split read mapping

  • Software interface: Command-line user interface

  • Language: C++

  • License: GNU General Public License v3.0

  • Cost: Free

  • Version name: v0.2.5b8

  • Credit: NGI/EBI fellowship 050-72-436 from Netherlands Genomics Initiative.

  • Input: -

  • Output: -

  • Contact: Kai Ye k.ye@lumc.nl, Zemin Ning zn1@sanger.ac.uk

  • Collection: -

  • Maturity: Stable

Publications

  • Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads.
  • Ye K, et al. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. 2009; 25:2865-71. doi: 10.1093/bioinformatics/btp394
  • https://doi.org/10.1093/bioinformatics/btp394
  • PMID: 19561018
  • PMC: PMC2781750

Download and documentation

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