… environmental applications, where identifying a particular … out of the total number of reads,
whereas Pathoscope calculates … (2) The diversity in strain composition in terms of taxonomic …

… metagenome samples from a given environment. In some cases… for the abundance of each
identified strain, we did not factor this … In general, PathoScope 2.0 produces some of the most …

… up to a year despite external, environmental perturbations. … and the creation of Clinical
Pathoscope that ultimately served as … framework for pathogen identification using a computational …

… de novo bacterial strain identification directly from shotgun … strains might be absent in
an extant clinical or environmental … command used was: pathoscope LIB -genomeFile <directory …

… We assessed whether the known strains identified above … strains might be absent in a
new clinical or environmental sample… command used was: pathoscope LIB -genomeFile <directory …

… patients in the hospital environment, the identification would be … the use of extensive
computational resources for de novo … the same identification and quantification using Pathoscope …

… enterica strains, and formulate strain identification as … assembly for multiple strains is
computationally challenging. In … microbial strains in metagenomic data from environmental or …

… The cloud computing environment used for this study are described in Supplementary Material
S2. A cutoff of 70% sequence identity was used for microbial read classification; this cutoff …

… the tools Qiime 2, Mothur, PathoScope 2, and Kraken 2 in … from PathoScope’s Bayesian
mixed modeling identification … that the target strain is not present in the reference database. …

… existing popular computational frameworks that utilize NGS … known genetic and environmental
etiologies. Microbiological … PathoScope 2.0 is designed to identify low abundant strains, …