Completion of draft bacterial genomes by long-read sequencing of synthetic metagenomes

Illumina technology currently dominates bacterial genomics due to its high read accuracy and low sequencing cost. However, the incompleteness of draft genomes generated by short Illumina reads limits their application in sensitive genomics analyses. Alternatively, long read sequencing can enable assembly of complete bacterial genomes, yet the high per-genome cost of sequencing limits the widespread use of these technologies in bacterial genomics. Here we developed a protocol for parallel sequencing and hybrid assembly of complete bacterial genomes using non-barcoded long-read sequencing of synthetic metagenomes, thus significantly decreasing the overall per-genome cost of sequencing.