WHO IS THERE AND WHAT ARE THEY DOING? AN AGILE AND COMPUTATIONALLY EFFICIENT FRAMEWORK FOR GENOME DISCOVERY AND ANNOTATION FROM METAGENOMIC BIG DATA

Microbes are more abundant than any other biological guild, and in any environment it is important to understand which organisms are present, what they are doing, and how they are doing it. In many environments a majority of the microbial community members cannot be cultured. Metagenomics is a powerful tool to directly probe uncultured genomes and understand the diversity of microbial communities using only their DNA sequences. Analyzing the taxonomic and functional profiles present in a microbial community from unannotated shotgun sequencing reads is one of the goals in metagenomics, with extremely valuable applications in biological research such as medicine, biofuel, and ecology. Currently available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keeps increasing.     This project aims to develop an agile and computationally efficient framework that integrates four methods that I have published (FOCUS, FOCUS2, Scaffold_builder, and SUPER-FOCUS) to recover, scaffold, and annotate genomes from metagenomes. In addition, the project aims to use the framework to create a database of new genomes from human microbiome and environmental samples.