Understanding Trivial Challenges of Microbial Genomics: an Assembly Example

The perceived “simplicity” of bacterial genomics (these genomes are small and easy to assemble) feeds the decentralized state of the field where computational analysis standards have been slow to evolve. This situation has a historical explanation. In cases of human, mouse, fly, worm and other model organisms there have been large sustained multinational genome sequencing efforts and analysis consortia such as the 1,000 genomes, ENCODE, modENCODE, GTEx and others. These resulted in development and proliferation of common tools, workflows, and data standards. This is not the case in microbiology. After the development of highly parallel sequencing methodologies in mid-2000s bacterial genomes no longer required initiatives of such scale. The flipside of this is the extreme heterogeneity of approaches to many well established microbial genomic analysis problems such as genome assembly. While competition amongst different methods is good, we argue that the quality of data analyses will improve if cutting edge tools are more accessible and microbiologists become more computationally savvy. Here we use genome assembly as an example to highlight current challenges and to provide a possible solution.