# Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads

## TL;DR

This paper evaluates how well different assembly methods work with nanopore sequencing data, comparing hybrid and non-hybrid approaches for bacterial genome assembly.

## Contribution

The study provides a benchmark of de novo assembly methods for nanopore reads, highlighting performance differences between hybrid and non-hybrid approaches.

## Key findings

- Hybrid methods perform well with lower nanopore coverage and depend more on NGS data quality.
- Non-hybrid methods can assemble E. coli genomes correctly at 40x nanopore coverage.
- Non-hybrid methods tailored for PacBio reads require higher coverage but run faster than nanopore-specific ones.

## Abstract

Recent emergence of nanopore sequencing technology set a challenge for the established assembly methods not optimized for the combination of read lengths and high error rates of nanopore reads. In this work we assessed how existing de novo assembly methods perform on these reads. We benchmarked three non-hybrid (in terms of both error correction and scaffolding) assembly pipelines as well as two hybrid assemblers which use third generation sequencing data to scaffold Illumina assemblies. Tests were performed on several publicly available MinION and Illumina datasets of E. coli K-12, using several sequencing coverages of nanopore data (20x, 30x, 40x and 50x). We attempted to assess the quality of assembly at each of these coverages, to estimate the requirements for closed bacterial genome assembly. Results show that hybrid methods are highly dependent on the quality of NGS data, but much less on the quality and coverage of nanopore data and perform relatively well on lower nanopore coverages. Furthermore, when coverage is above 40x, all non-hybrid methods correctly assemble the E. coli genome, even a non-hybrid method tailored for Pacific Bioscience reads. While it requires higher coverage compared to a method designed particularly for nanopore reads, its running time is significantly lower.