Treat: A bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

Yan Asmann, Sumit Middha, Asif Hossain, Saurabh Baheti, Ying Li, High Seng Chai, Zhifu D Sun, Patrick H. Duffy, Ahmed A. Hadad, Asha Nair, Xiaoyu Liu, Yuji Zhang, Eric W Klee, Krishna R Kalari, Jean-Pierre Kocher

Research output: Contribution to journalArticle

44 Citations (Scopus)

Abstract

TREAT (Targeted RE-sequencing Annotation Tool) is a tool for facile navigation and mining of the variants from both targeted resequencing and whole exome sequencing. It provides a rich integration of publicly available as well as in-house developed annotations and visualizations for variants, variant-hosting genes and host-gene pathways. Availability and implementation: TREAT is freely available to non-commercial users as either a stand-alone annotation and visualization tool, or as a comprehensive workflow integrating sequencing alignment and variant calling. The executables, instructions and the Amazon Cloud Images of TREAT can be downloaded at the website: http://ndc.mayo.edu/mayo/research/ biostat/stand-alone-packages.cfm.

Original languageEnglish (US)
Article numberbtr612
Pages (from-to)277-278
Number of pages2
JournalBioinformatics
Volume28
Issue number2
DOIs
StatePublished - Jan 2012

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Exome
Bioinformatics
Computational Biology
Sequencing
Annotation
Visualization
Workflow
Genes
Gene
Research
Work Flow
Navigation
Mining
Pathway
Alignment
Availability

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Treat : A bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. / Asmann, Yan; Middha, Sumit; Hossain, Asif; Baheti, Saurabh; Li, Ying; Chai, High Seng; Sun, Zhifu D; Duffy, Patrick H.; Hadad, Ahmed A.; Nair, Asha; Liu, Xiaoyu; Zhang, Yuji; Klee, Eric W; Kalari, Krishna R; Kocher, Jean-Pierre.

In: Bioinformatics, Vol. 28, No. 2, btr612, 01.2012, p. 277-278.

Research output: Contribution to journalArticle

Asmann, Y, Middha, S, Hossain, A, Baheti, S, Li, Y, Chai, HS, Sun, ZD, Duffy, PH, Hadad, AA, Nair, A, Liu, X, Zhang, Y, Klee, EW, Kalari, KR & Kocher, J-P 2012, 'Treat: A bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data', Bioinformatics, vol. 28, no. 2, btr612, pp. 277-278. https://doi.org/10.1093/bioinformatics/btr612
Asmann, Yan ; Middha, Sumit ; Hossain, Asif ; Baheti, Saurabh ; Li, Ying ; Chai, High Seng ; Sun, Zhifu D ; Duffy, Patrick H. ; Hadad, Ahmed A. ; Nair, Asha ; Liu, Xiaoyu ; Zhang, Yuji ; Klee, Eric W ; Kalari, Krishna R ; Kocher, Jean-Pierre. / Treat : A bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. In: Bioinformatics. 2012 ; Vol. 28, No. 2. pp. 277-278.
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