Now showing items 1-10 of 12
Assembly complexity of prokaryotic genomes using short reads
Background: De Bruijn graphs are a theoretical framework underlying several modern genome assembly programs, especially those that deal with very short reads. We describe an application of de Bruijn graphs to analyze the ...
Searching for SNPs with cloud computing
(Springer Nature, 2009-11-20)
As DNA sequencing outpaces improvements in computer speed, there is a critical need to accelerate tasks like alignment and SNP calling. Crossbow is a cloud-computing software tool that combines the aligner Bowtie and the ...
Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection
(Springer Nature, 2016-07-08)
Longitudinal studies of the lung microbiome are challenging due to the invasive nature of sample collection. In addition, studies of the lung microbiome in human disease are usually performed after disease onset, limiting ...
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
(Springer Nature, 2011-07-27)
A major goal of metagenomics is to characterize the microbial composition of an environment. The most popular approach relies on 16S rRNA sequencing, however this approach can generate biased estimates due to differences ...
Outlier detection in BLAST hits
(Springer Nature, 2018-03-22)
An important task in a metagenomic analysis is the assignment of taxonomic labels to sequences in a sample. Most widely used methods for taxonomy assignment compare a sequence in the sample to a database of known sequences. ...
We are what we eat: how the diet of infants affects their gut microbiome
(Springer Nature, 2012-04-30)
Simultaneous analysis of the gut microbiome and host gene expression in infants reveals the impact of diet (breastfeeding versus formula) on host-microbiome interactions.
Automated ensemble assembly and validation of microbial genomes
(Springer Nature, 2014-05-03)
The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the ...
Exploiting sparseness in de novo genome assembly
(Springer Nature, 2012-04-19)
The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. In this paper, we demonstrate that constructing a sparse ...
Genome assembly forensics: finding the elusive mis-assembly
(Springer Nature, 2008-03-14)
We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation ...
Genomic characterization of the Yersinia genus
(Springer Nature, 2010-01-04)
New DNA sequencing technologies have enabled detailed comparative genomic analyses of entire genera of bacterial pathogens. Prior to this study, three species of the enterobacterial genus Yersinia that cause invasive human ...