Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center

Methods Mol Biol. 2018;1704:79-101. doi: 10.1007/978-1-4939-7463-4_4.

Abstract

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, www.patricbrc.org ) 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.

Keywords: Annotation; Archaea; Assembly; Bacteria; Bioinformatics; Comparative genomics.

Publication types

  • Comparative Study
  • Review

MeSH terms

  • Bacteria / genetics*
  • Computational Biology
  • Databases, Genetic*
  • Genome, Bacterial*
  • Genomics / methods*
  • Internet
  • Molecular Sequence Annotation*
  • Software*
  • Statistics as Topic