# Gapless near Telomer-to-Telomer Assembly of Neurospora intermedia, Aspergillus oryzae, and Trichoderma asperellum from Nanopore Simplex Reads

## TL;DR

This paper shows how to create high-quality fungal genome assemblies using only Nanopore sequencing data, reducing the need for multiple sequencing platforms.

## Contribution

The study introduces a workflow using haplotype-aware error correction to achieve gapless fungal genome assemblies from Nanopore simplex reads.

## Key findings

- Gapless assemblies were achieved for three fungal species using only Nanopore sequencing.
- The T. asperellum assembly was fully telomere-to-telomere, while others were near-telomere-to-telomere.
- The workflow achieved BUSCO scores over 98% for all three genomes.

## Abstract

Assembling high-quality fungal genomes, specifically telomere-to-telomere (T2T) gapless assemblies, often necessitates the integration of multiple sequencing platforms. This requirement poses a limitation on the number of fungal genomes that can feasibly be generated within a single project. Here, we demonstrate that haplotype-aware error correction (HERRO) of Oxford Nanopore simplex reads enables the generation of high-quality assemblies from a single sequencing platform. We present an automated Snakemake workflow that, without manual intervention, produced gapless genome assemblies for industrially relevant strains: Neurospora intermedia NRRL 2884, Trichoderma asperellum TA1, and Aspergillus oryzae CBS 466.91, each achieving complete BUSCO (Benchmarking Universal Single-Copy Orthologs) scores exceeding 98%. Among these, only the T. asperellum assembly yielded a fully telomere-to-telomere gapless genome, while the N. intermedia and A. oryzae assemblies were gapless but near-telomere-to-telomere. Manual curation was required for the mitochondrial genome assembly of N. intermedia.