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Genomon-ITDetector

Genomon-ITDetector

Genomon-ITDetector is a tool to discover regions duplicated in tandem specifically in cancer genome sequencing data sets. The Genomon-ITDetector depends on the following externals tools: 1. blat (Ver. 34x13), 2. bedtools (Ver. 2.14.3), 3. CAP3 (Ver.Date: 12/21/07), 4. fasta36 (Ver. 3.5c), 5. SAMtools Ver. 0.1.18), and 6. refGene.txt, knownGene.txt, ensGene.txt and simpleRepeat.txt from the UCSC.

Topic

Oncology; DNA; Sequence analysis; DNA mutation

Details

  • Operation: Repeat sequence detection
  • Software interface: Command-line user interface
  • Language: Perl
  • Operating system: Linux
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Credit: Integrative Systems Understanding of Cancer for Advanced Diagnosis, Therapy and Prevention, the Ministry of Education, Culture, Sports, Science and Technology, Japan.
  • Contact: kchiba _at_ hgc.jp | yshira _at_ hgc.jp
  • Collection: -

Publications

Chiba K, Shiraishi Y, Nagata Y, Yoshida K, Imoto S, Ogawa S, Miyano S "Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data." Bioinformatics 2015; 31(1):116-8 https://doi.org/10.1093/bioinformatics/btu593
PMID: 25192740


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