Jan 26, 2019

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

BioRxiv : the Preprint Server for Biology
Nicola De MaioThe REHAB consortium

Abstract

Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly. Long read sequencing greatly assists with resolving complex bacterial genomes, particularly when combined with short-read Illumina data (hybrid assembly); however, it is not clear how different long-read sequencing methods impact on assembly accuracy. Relative automation of the assembly process is also crucial to facilitating high-throughput complete bacterial genome reconstruction, avoiding multiple bespoke filtering and data manipulation steps. In this study, we compared hybrid assemblies for 20 bacterial isolates, including two reference strains, using Illumina sequencing and long reads from either Oxford Nanopore Technologies (ONT) or from SMRT Pacific Biosciences (PacBio) sequencing platforms. We chose isolates from the Enterobacteriaceae family, as these frequently have highly plastic, repetitive genetic structures and complete genome reconstruction for these species is relevant for a precise understanding of the epidemiology of antimicrobial resistance. We de novo assembled genomes using the hybrid assembler Unicycler and compared different read processing strateg...Continue Reading

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Mentioned in this Paper

Study
Enterobacteriaceae
Genome
Reconstructive Surgical Procedures
Nucleic Acid Sequencing
ONT-10
High Throughput Analysis
Resistance Process
Isolate - Microorganism
Molecular Genetic Technique

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