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TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data.

ABSTRACT:

Unlabelled

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.

SUBMITTER: Asmann YW

PROVIDER: S-EPMC3259432 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature

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TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data.

Asmann Yan W YW Middha Sumit S Hossain Asif A Baheti Saurabh S Li Ying Y Chai High-Seng HS Sun Zhifu Z Duffy Patrick H PH Hadad Ahmed A AA Nair Asha A Liu Xiaoyu X Zhang Yuji Y Klee Eric W EW Kalari Krishna R KR Kocher Jean-Pierre A JP

Bioinformatics (Oxford, England) 20111115 2

<h4>Unlabelled</h4>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.<h4>Availability and implementation</h4>TREAT is freely available to non-commercial users as either a stand-alone annotation and visualization ...[more]

PMID: 22088845

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