NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats
JW Sahl, D Lemmer, J Travis, JM Schupp… - Microbial …, 2016 - microbiologyresearch.org
Whole-genome sequencing (WGS) of bacterial isolates has become standard practice in
many laboratories. Applications for WGS analysis include phylogeography and molecular …
many laboratories. Applications for WGS analysis include phylogeography and molecular …
Solving the problem of comparing whole bacterial genomes across different sequencing platforms
Whole genome sequencing (WGS) shows great potential for real-time monitoring and
identification of infectious disease outbreaks. However, rapid and reliable comparison of …
identification of infectious disease outbreaks. However, rapid and reliable comparison of …
SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology
The recent widespread application of whole-genome sequencing (WGS) for microbial
disease investigations has spurred the development of new bioinformatics tools, including a …
disease investigations has spurred the development of new bioinformatics tools, including a …
BacSeq: A user-friendly automated pipeline for whole-genome sequence analysis of bacterial genomes
A Chukamnerd, K Jeenkeawpiam, S Chusri… - Microorganisms, 2023 - mdpi.com
Whole-genome sequencing (WGS) of bacterial pathogens is widely conducted in
microbiological, medical, and clinical research to explore genetic insights that could impact …
microbiological, medical, and clinical research to explore genetic insights that could impact …
TORMES: an automated pipeline for whole bacterial genome analysis
NM Quijada, D Rodríguez-Lázaro, JM Eiros… - …, 2019 - academic.oup.com
Abstract Motivation The progress of High Throughput Sequencing (HTS) technologies and
the reduction in the sequencing costs are such that Whole Genome Sequencing (WGS) …
the reduction in the sequencing costs are such that Whole Genome Sequencing (WGS) …
Comparison of whole genome (wg-) and core genome (cg-) MLST (BioNumericsTM) versus SNP variant calling for epidemiological investigation of Pseudomonas …
DS Blanc, B Magalhães, I Koenig, L Senn… - Frontiers in …, 2020 - frontiersin.org
Whole genome sequencing (WGS) is increasingly used for epidemiological investigations of
pathogens. While SNP variant calling is currently considered as the most suitable method …
pathogens. While SNP variant calling is currently considered as the most suitable method …
Interpreting whole-genome sequence analyses of foodborne bacteria for regulatory applications and outbreak investigations
AW Pightling, JB Pettengill, Y Luo, JD Baugher… - Frontiers in …, 2018 - frontiersin.org
Whole-genome sequence (WGS) analysis has revolutionized the food safety industry by
enabling high-resolution typing of foodborne bacteria. Higher resolving power allows …
enabling high-resolution typing of foodborne bacteria. Higher resolving power allows …
Beginner's guide to comparative bacterial genome analysis using next-generation sequence data
DJ Edwards, KE Holt - Microbial informatics and experimentation, 2013 - Springer
High throughput sequencing is now fast and cheap enough to be considered part of the
toolbox for investigating bacteria, and there are thousands of bacterial genome sequences …
toolbox for investigating bacteria, and there are thousands of bacterial genome sequences …
PGAT: a multistrain analysis resource for microbial genomes
MJ Brittnacher, C Fong, HS Hayden, MA Jacobs… - …, 2011 - academic.oup.com
Abstract Motivation: The Prokaryotic-genome Analysis Tool (PGAT) is a web-based
database application for comparing gene content and sequence across multiple microbial …
database application for comparing gene content and sequence across multiple microbial …
[HTML][HTML] A step-by-step beginner's protocol for whole genome sequencing of human bacterial pathogens
SS Gautam, KC Rajendra, KWC Leong… - Journal of biological …, 2019 - ncbi.nlm.nih.gov
Bacterial whole genome sequencing (WGS) is becoming a widely-used technique in
research, clinical diagnostic, and public health laboratories. It enables high resolution …
research, clinical diagnostic, and public health laboratories. It enables high resolution …