Version 2: Sequenoscope: A Modular Tool for Nanopore Adaptive Sequencing Analytics and Beyond

This paper presents Sequenoscope a bioinformatics pipeline for analyzing Oxford Nanopore Technologies (ONT) adaptive sampling sequencing data. Sequenoscope features three main modules: filter_ONT for filtering raw reads and creating a FASTQ file with a subset of reads for further analyses, analyze for generating sequencing and read mapping statistics against the provided reference taxon sequences, and plot for interactive data summarization, comparison, and visualization between two datasets/test conditions. Here we demonstrate the ability of the pipeline to analyze ONT adaptive sampling sequence data and provide examples of the outputs users can expect using data we generated. Adaptive sampling was performed on two ZymoBIOMICS Microbial Community DNA Standards (Cat# D6311 and D6306)  with targeted depletions of Listeria monocytogenes. By comparing the test and control experimental data in FASTQ file from the sequencing runs, Sequenoscope showed that depletion of L. monocytogenes was successful by providing users with parameters to compare such as taxon coverage, read length, and types of pore-level decisions made during sequencing. Although Sequenoscope was designed for ONT adaptive sampling data analysis, it can also be used to compare any two experimental conditions and supports short-read data from other sequencing platforms.