Matching excellence: Oxford Nanopore Technologies' rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content.

ABSTRACT: The reconstruction of complete bacterial genomes is essential for microbial research, offering insights into genetic content, ontology and regulation. While Pacific Biosciences (PacBio) provides high-quality genomes, its cost remains a limitation. Oxford Nanopore Technologies (ONT) offers long reads at a lower cost, yet its error rate raises scepticism. Recent ONT advancements, such as new Flow cells (R10.4.1), chemistry (V14) and duplex mode, improve data quality. Our study compares ONT with PacBio and Illumina, including hybrid data. We used Propionibacterium freudenreichii, a bacterium with a genome known for being difficult to reconstruct. By combining data from ONT's Native Barcoding and a custom-developed BARSEQ method, we achieved high-quality, near-perfect genome assemblies.

SUBMITTER: Soto-Serrano A 

PROVIDER: S-EPMC11649196 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature