geneious mapper  (Biotechnology Information)

Journal: Applied and Environmental Microbiology

Article Title: Evidence of in vitro mecB -mediated β-lactam antibiotic resistance transfer to Staphylococcus aureus from Macrococcus psychrotolerans sp. nov., a psychrophilic bacterium from food-producing animals and human clinical specimens

doi: 10.1128/aem.01652-24

Figure Lengend Snippet: Genetic map of linear plasmid p19Msa1099_9 (GenBank accession number CP079956.2 ). Arrows show the position and orientation of predicted coding regions. The predicted genes are color-coded according to the legend. The sequences of physical ends of the hairpin plasmid are shown below the gene map. The mapping of sequencing reads longer than 10 kb to the assembled plasmid sequence revealed a centrally symmetric alignment of reads to the covalently closed ends of the hairpin plasmid. These reads resulted from the unfolding of the terminal hairpin structure during Oxford Nanopore sequencing technology (ONT) as it passed through the nanopore, and therefore, the unmapped parts correspond to the complementary strand (highlighted by a red dotted line). The mean coverage calculated from all ONT reads by Geneious mapper was 881× with a standard deviation of 215.

Article Snippet: Long sequencing reads were mapped to the reference chromosomal and plasmid sequences using the built-in Geneious Mapper (Minimum mapping quality: 10) in Geneious Prime v2024.0.5 (GraphPad Software, New Zealand).

Techniques: Plasmid Preparation, Sequencing, Nanopore Sequencing, Standard Deviation