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Detects breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-generation sequence data. Pindel uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

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Command line interface
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Unix/Linux, Mac OS, Windows
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  • (Ye et al., 2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics.
    PMID: 19561018
  • (Lim et al., 2013) Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance. Briefings in bioinformatics.
    PMID: 22648964
  • (Treangen and Salzberg, 2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature reviews Genetics.
    PMID: 22124482
  • (Cao et al., 2014) Sequencing technologies and tools for short tandem repeat variation detection. Briefings in bioinformatics.
    PMID: 24504770

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