TCGA-Assembler 2: Software Pipeline for Automatic Retrieval, Processing, and Integration of TCGA/CPTAC Data

Introduction:

TCGA-Assembler 2 is an open-source, freely available tool that automatically downloads, assembles and processes public The Cancer Genome Atlas (TCGA) data and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) data of TCGA samples. It facilitates downstream data analysis by relieving investigators from the burdens of data preparation. TCGA-Assembler 2 includes two modules. Module A acquires public TCGA data from the Genomic Data Commons (GDC) of the U.S. National Cancer Institute and assembles individual data files into locally stored data tables. It can also acquire mass spectrometry proteomics data of TCGA samples generated by the CPTAC. Module B fulfills various data processing needs to prepare them for downstream analysis. TCGA-Assembler 2 is licensed under the GPL version 3 and can be distributed under GPL version 3.

GitHub:

TCGA-Assembler 2 software package can be downloaded from GitHub at https://github.com/compgenome365/TCGA-Assembler-2

Contact:

Yitan Zhu: zhuyitan@gmail.com Yuan Ji: koaeraser@gmail.com

Distribution of TCGA-Assembler Users:

Since its first release in Feb. 2014, TCGA-Assembler has been downloaded and used by researchers from different countries and regions all over the world. Click here to see the details.

Country	Number of Users	Institutions

Please cite:

Wei, L., Jin, Z., Yang, S., Xu, Y., Zhu, Y. and Ji, Y. "TCGA-Assembler 2: Software Pipeline for Retrieval and Processing of TCGA/CPTAC Data." Bioinformatics (2017). https://doi.org/10.1093/bioinformatics/btx812
Zhu, Y., Qiu, P. and Ji, Y., 2014. TCGA-assembler: open-source software for retrieving and processing TCGA data. Nature methods, 11(6), pp.599-600.