July 7, 2019  |  

Assembly, annotation, and comparative genomics in PATRIC, the All Bacterial Bioinformatics Resource Center.

Authors: Wattam, Alice R and Brettin, Thomas and Davis, James J and Gerdes, Svetlana and Kenyon, Ronald and Machi, Dustin and Mao, Chunhong and Olson, Robert and Overbeek, Ross and Pusch, Gordon D and Shukla, Maulik P and Stevens, Rick and Vonstein, Veronika and Warren, Andrew and Xia, Fangfang and Yoo, Hyunseung

In the "big data" era, research biologists are faced with analyzing new types that usually require some level of computational expertise. A number of programs and pipelines exist, but acquiring the expertise to run them, and then understanding the output can be a challenge.The Pathosystems Resource Integration Center (PATRIC, ) has created an end-to-end analysis platform that allows researchers to take their raw reads, assemble a genome, annotate it, and then use a suite of user-friendly tools to compare it to any public data that is available in the repository. With close to 113,000 bacterial and more than 1000 archaeal genomes, PATRIC creates a unique research experience with "virtual integration" of private and public data. PATRIC contains many diverse tools and functionalities to explore both genome-scale and gene expression data, but the main focus of this chapter is on assembly, annotation, and the downstream comparative analysis functionality that is freely available in the resource.

Journal: Methods in molecular biology
DOI: 10.1007/978-1-4939-7463-4_4
Year: 2018

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