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TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data
Lin Wei1, Zhilin Jin2, Shengjie Yang1
1Program of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL 60201, USA.
Bioinformatics (Oxford, England)
|December 23, 2017
Summary
TCGA-Assembler 2 (TA2) is a new software tool that integrates cancer genomics and proteomics data from the Genomic Data Commons (GDC) and Clinical Proteomic Tumor Analysis Consortium (CPTAC). This tool facilitates reproducible cancer research by simplifying data access for over 2000 researchers globally.
Area of Science:
- Genomics
- Proteomics
- Bioinformatics
Background:
- The Cancer Genome Atlas (TCGA) program generated extensive cancer genomics data, necessitating efficient retrieval and processing tools.
- Data migration from the TCGA portal to the Genomic Data Commons (GDC) and the generation of new proteomics data by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) created a need for integrated data access.
Purpose of the Study:
- To develop an automated software pipeline for downloading and integrating TCGA, GDC, and CPTAC data.
- To enhance user experience and software performance for accessing multi-omics cancer data.
Main Methods:
- Development of TCGA-Assembler 2 (TA2), an updated software pipeline.
- Implementation of mechanisms to retrieve and integrate data from both GDC and CPTAC repositories.
Main Results:
- TA2 enables automatic download and integration of diverse cancer datasets.
- The software has supported over 2000 researchers across 64 countries in accessing TCGA and CPTAC data.
- Substantial improvements in functionality, user experience, and performance were achieved.
Conclusions:
- TA2 facilitates reproducible research by providing unified access to TCGA and CPTAC data.
- The tool continues to support both existing and new users in their cancer genomics and proteomics research endeavors.
