… This review provides a historical perspective on the use of … the major steps in phylogenomic
pipelines used for pathogen … Real-time genomic epidemiological evaluation of human …

… All of these hqSNP pipelines can theoretically identify all the single nucleotide … in a genome.
In addition, parameter settings in both the CFSAN and the Lyve-SET pipelines can be used …

… complete genomes (eg, CFSAN, SPANDx, Lyve-set)… review of its name/description. With
the rapid increase in available E. coli and related genomes and a shifting view of their phylogeny…

… The downloaded sra files were converted into fastq files; then, Lyve-SET was used to extract
… The procedure is the same as described above, Lyve-SET was used to extract SNPs and …

… comparative studies to eventually contribute to a justified use of a specific WGS data analysis
… Therefore, we evaluate the reproducibility of a pipeline based on the maximal genetic …

… new pipelines benchmarked on their own datasets with limited comparisons to previously
published pipelines. In this study, Snpdragon, a fast and accurate SNP calling pipeline is …

… Genomic epidemiology, the use of genomic data in outbreak investigations and disease …
pipeline (BioNumerics) and open-source high-quality SNP-based pipelines (CFSAN, Lyve-SET)…

… pipelines for SNPs analysis incorporated quality-based trimming, fixed-width trimming, or
both. The Lyve-SET SNPs pipeline … In summary, six of the healing pipelines healed reads …

… In most cases, the computational pipeline of WGS data analysis can … genome assembly,
genome characterization, comparative genomics, and inference of phylogeny or phylogenomics. …

… tracking, microbial epidemiology, and phylogenomics. While the major … I am unaware of
other programs or pipelines that meet all of … Similarly, SNVPhyl, RealPhy, and Lyve-SET require …