Nanopore Adaptive Sampling: Zymobiomics Microbial Community Standards Sequenoscope Tool Comparison Study
Sequenoscope is a tool that aims to provide researchers with a streamlined and efficient workflow for processing and analyzing sequencing data, enabling them to gain valuable insights into their datasets. The following data sets were generated to assess adaptive sampling effectiveness between test and control read sets. Sequenoscope is available at https://github.com/phac-nml/sequenoscope.The two primary microbial standards were sequenced with standard and log abundance distribution of microbial communities. The ZymoBIOMICS Microbial Community Standard II (Log Distribution) catalog #D6311, mapped to barcodes 1 to 3, and the ZymoBIOMICS Microbial Community Standard II catalog #D6300, mapped to barcodes 4 to 6. The Log Distribution standard composition was as follows: Listeria monocytogenes dominated with a prevalence of 89.1%, followed by Pseudomonas aeruginosa at 8.9%. Other microbes, such as Bacillus subtilis and Saccharomyces cerevisiae, were present at 0.89%. At lower percentages, Escherichia coli and Salmonella enterica were each at 0.089%, with Lactobacillus fermentum at 0.0089%. The least prevalent were Enterococcus faecalis, Cryptococcus neoformans, and Staphylococcus aureus, with concentrations of 0.00089%, 0.00089%, and 0.000089%, respectively. On the other hand, the ZymoBIOMICS Microbial Community Standard, linked with barcodes 4 to 6, followed an even distribution approach with the exception of two species. Here, Listeria monocytogenes, Pseudomonas aeruginosa, and Bacillus subtilis, had an equal prevalence of 12% with the exception of Saccharomyces cerevisiae and Cryptococcus neoformans, each present at 2%.