Comparison of Automated Pipelines for Nanopore 16S Sequencing Data Analysis of Human Gut Microbiota Samples

Next Generation Sequencing (NGS) enables characterization of complex microbial communities through metagenomic techniques. Metagenomics generally employs sequencing of multiple samples at once, through barcoding techniques, with subsequent reads of each sample being demultiplexed by specialized software. Third generation NGS equipment such as the Oxford Nanopore (ONT) technology has been developed to reduce costs, turnaround time and complex bioinformatics. For ONT, several bioinformatic workflows are available, with various tools for each step such as demultiplexing, classification of reads, polishing, mapping and visualization, which are successively applied on raw data. The performance and results of the workflows vary, especially considering the fact that ONT presents a 10-15% error rate, with short reads and around 5% with long reads. Here, we compare the results of two different workflows (Nanopore’s EPI2ME and NanoCLUST platforms) for real-world 16S human gut microbiota samples.