Complete Genomics Analysis Tools (CGA™ Tools) are a set of open source software tools for downstream analysis of sequencing data produced by Complete Genomics. These tools focus on multi-genome comparisons and format conversion, for example to VCF and SAM formats. Customers can use these tools to conduct various analyses including family-based analysis or case-control analysis.
Analysis functionality includes:
- Genome comparison tools — compare different types of variant calls between genomes
- Format conversion tools — export data into other standard formats for analysis
- Filtering and annotation tools — manipulate variant files
- Reference tools — help build a copy of the reference genome for other CGA Tools analyses
The CGA Tools package is freely available as pre-compiled binary distributions for 64-bit Linux and Mac OS X platforms. Installing from the provided source code provides access to the CGA Tools C++ APIs. The most popular CGA Tools commands are also published in Mac and Linux repositories in the Galaxy Tool Shed, allowing users to harness the graphical interface provided by Galaxy to develop workflows that incorporate the tools.
Download CGA Tools and find additional documentation here.