Now showing items 1-5 of 5
Uncovering missed indels by leveraging unmapped reads
(Springer Nature, 2019-07-31)
In current practice, Next Generation Sequencing (NGS) applications start with mapping/aligning short reads to the reference genome, with the aim of identifying genetic variants. Although existing alignment tools have shown ...
vi-HMM: a novel HMM-based method for sequence variant identification in short-read data
Abstract Background Accurate and reliable identification of sequence variants, including single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (INDELs), ...
Effects of Dairy Manure-Based Amendments and Soil Texture on Lettuce-and Radish-Associated Microbiota and Resistomes
(American Society for Microbiology, 2019)
Dairy cattle are routinely treated with antibiotics, and the resulting manure or composted manure is commonly used as a soil amendment for crop production, raising questions regarding the potential for antibiotic resistance ...
NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes
Background Direct and indirect selection pressures imposed by antibiotics and co-selective agents and horizontal gene transfer are fundamental drivers of the evolution and spread of antibiotic resistance. ...
Comparison of Whole-Genome Sequences of Legionella pneumophila in Tap Water and in Clinical Strains, Flint, Michigan, USA, 2016
(Centers for Disease Control and Prevention, 2019-11)
During the water crisis in Flint, Michigan, USA (2014–2015), 2 outbreaks of Legionnaires’ disease occurred in Genesee County, Michigan. We compared whole-genome sequences of 10 clinical Legionella pneumophila isolates ...