Development of Modular and Standardized Nextflow Workflows for Oxford Nanopore Data Analysis

BACKGROUND AND QUESTION 
Nanopore technology (ONT) is a third-generation sequencing technology becoming increasingly competitive in the sequencing market. Following Sanger and NGS sequencing methods, which rely on fragmentation and subsequent amplification to read DNA, third-generation sequencing technologies sequence a single DNA molecule directly. 

This advancement in sequencing technology comes with several key benefits. First, ONT technology can produce extremely long reads, making it a powerful tool for de novo genome assembly, structural variant identification, and traversing repetitive genomic regions. [1] Secondly, ONT has created compact, cost-effective sequencing devices such as the MinION and Flongle. These portable devices allow field-based, real-time data generation, providing valuable resources for rapid diagnostics and outbreak tracking. 

Historically, ONT has had much higher sequencing error rates than NGS sequencing (ONT, 1/50 bp-1/100 bp and Illumina, 1/1000 bp). [2,3] However, advances in equipment and software have drastically improved ONT’s error rate performance; some researchers recently claim they have achieved fidelities rivaling Illumina’s. With these advances, ONT is starting to present a viable alternative to NGS sequencing, especially in cases of de novo assembly, as well as when cost and time represent a critical factor.