Assembling metagenomes, one community at a time

Assembling large, complex environmental metagenomes

The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning , to make large metagenome assembl...

Assembling molecular electronic junctions one molecule at a time.

Diffusion of metal atoms onto a molecular monolayer attached to a conducting surface permits electronic contact to the molecules with minimal heat transfer or structural disturbance. Surface-mediated metal deposition (SDMD) involves contact between "cold" diffusing metal atoms and molecules, due to shielding of the molecules from direct exposure to metal vapor. Measurement of the current throug...

Assembling the Marine Metagenome, One Cell at a Time

The difficulty associated with the cultivation of most microorganisms and the complexity of natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction of representative taxa using cultivation or metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality genome assemblies of two uncultured, numerically...

CAREER: ABI: Assembling Extremely Large Metagenomes

One Loop at a Time

Classic techniques for proving termination require the identification of a measure mapping program states to the elements of a well founded domain and to show that this measure decreases with each iteration of a loop in the program. This is a global termination condition — there is a single measure which must be shown to decrease over all of the loops in the program. In this abstract we look at...