Learn More
The paucity of enzymes that efficiently deconstruct plant polysaccharides represents a major bottleneck for industrial-scale conversion of cellulosic biomass into biofuels. Cow rumen microbes specialize in degradation of cellulosic plant material, but most members of this complex community resist cultivation. To characterize biomass-degrading genes and(More)
MOTIVATION Researchers need general purpose methods for objectively evaluating the accuracy of single and metagenome assemblies and for automatically detecting any errors they may contain. Current methods do not fully meet this need because they require a reference, only consider one of the many aspects of assembly quality or lack statistical justification,(More)
Grouping large genomic fragments assembled from shotgun metagenomic sequences to deconvolute complex microbial communities, or metagenome binning, enables the study of individual organisms and their interactions. Because of the complex nature of these communities, existing metagenome binning methods often miss a large number of microbial species. In(More)
<i>De novo</i> whole genome assembly reconstructs genomic sequences from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMer, the first high-quality end-to-end <i>de novo</i> assembler designed for extreme scale analysis, via efficient parallelization of the(More)
Advances in nanopore sequencing technology have enabled investigation of the full catalogue of covalent DNA modifications. We present the first algorithm for the identification of modified nucleotides without the need for prior training data along with the open source software implementation, nanoraw. Nanoraw accurately assigns contiguous raw nanopore(More)
We present software that reconstructs genomes from shotgun metagenomic sequences using a reference-independent approach. This method permits the identification of OTUs in large complex communities where many species are unknown. Binning reduces the complexity of a metagenomic dataset enabling many downstream analyses previously unavailable. In this study we(More)
Virophages are small viruses that co-infect eukaryotic cells alongside giant viruses (Mimiviridae) and hijack their machinery to replicate. While two types of virophages have been isolated, their genomic diversity and ecology remain largely unknown. Here we use time series metagenomics to identify and study the dynamics of 25 uncultivated virophage(More)
De novo genome assembly is one of the most important and challenging computational problems in modern genomics; further, it shares algorithms and communication patterns important to other graph analytic and irregular applications. Unlike simulations, it has no floating point arithmetic and is dominated by small memory transactions within and between(More)
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code. Genome(More)