Real-time sequencing analysis with Nextflow

A unique feature of Oxford Nanopore Technologies’ sequencing devices is the ability to output sequencing data in a real-time stream. Here we show how this unique ability can be coupled with Nextflow for file-based streaming bioinformatics. We create a server/client implementation of the kraken2 metagenomics classifier to classify sequencing reads as they are produced and provide an updating view of species abundance and diversity. We discuss how such analysis can be combined with Oxford Nanopore’s adaptive sampling technology to augment and optimise the sequencing process to search for rarer species present in the sample. Finally we demonstrate how these analyses are open to all scientist through Oxford Nanopore’s EPI2ME desktop interface.