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

• DOI: 10.1099/mgen.0.000294
• Publication Date: 2019-09-24T10:12:53Z
• Authors: Nicola De Maio; Liam P. Shaw; Alasdair Hubbard; Sophie George; Nicholas D. Sande...; Jeremy Swann; Ryan Wick; Manal AbuOun; Emma Stubberfield; Sarah J. Hoosdally; Derrick W. Crook; Timothy E. A. Peto; Anna E. Sheppard; Mark J. Bailey; Daniel S. Read; Muna F. Anjum; A. Sarah Walker; Nicole Stoesser
• Keywords: Sequence assembly; Hybrid genome assembly; Illumina dye sequencing; Bacterial genome size; Minion

Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete assembly. Long-read greatly assists with resolving complex genomes, particularly when combined short-read data (hybrid assembly). However, it is clear how different long-read methods affect hybrid assembly accuracy. Relative automation of the process also crucial to facilitating high-throughput reconstruction, avoiding multiple bespoke filtering manipulation steps. In this study, we compared assemblies for 20 isolates, including two reference strains, using long from either Oxford Nanopore Technologies (ONT) or SMRT Pacific Biosciences (PacBio) platforms. We chose isolates family Enterobacteriaceae, as these frequently have highly plastic, repetitive genetic structures, reconstruction species relevant a precise understanding epidemiology antimicrobial resistance. de novo assembled genomes assembler Unicycler read processing strategies, well comparing long-read-only Flye followed by polishing Pilon. Hybrid PacBio ONT facilitated high-quality was superior approach evaluated respect accuracy completeness. Combining fully resolved most without additional manual steps, at lower consumables cost per isolate in our setting. Automated powerful tool