Biome representational in silico karyotyping

Project ID
FG-315
Project Categories
Non-Life Science
Completed
Abstract
Characterization of complex metagenomics remains a challenge both with biochemical techniques and bioinformatics. We have designed a novel modification of digital karyotyping-biome representational in silico karyotyping (BRISK)-as a general technique for analyzing a defined representation of all DNA present in a sample. BRISK utilizes a Type IIB DNA restriction enzyme to create a defined representation of 27-mer DNAs in a sample. Massively parallel sequencing of this representation allows for construction of high-resolution karyotypes and identification of multiple species within a biome. We propose to develop a distributed bioinformatics processing chain using Hadoop to perform complex analyses of microbiomes with the sequencing output from BRiSK.
Use of FutureSystems
Need long-term access to large computing capacities for handling next generation sequencing data.
Scale of Use
A few VMs for development and experiments of scaling. Then possibly more computing resources to process and analyze BRISK output data.