Low-input single molecule HiFi sequencing for metagenomic samples

Author(s): Ashby, Meredith and Chakraborty, Shreyasee and Portik, Daniel and Baybayan, Primo, Korlach, Jonas, Nurk, Sergey, Koren, Sergey, Lolans, Karen and Gratalo, Dawn and Driscoll, Mark and Quince, Christopher and Eren, A. Murat and Phillippy, Adam M.

HiFi sequencing on the PacBio Sequel II System enables complete microbial community profiling of complex metagenomic samples using whole genome shotgun sequences. With HiFi sequencing, highly accurate long reads overcome the challenges posed by the presence of intergenic and extragenic repeat elements in microbial genomes, thus greatly improving phylogenetic profiling and sequence assembly. Recent improvements in library construction protocols enable HiFi sequencing starting from as low as 5 ng of input DNA. Here, we demonstrate comparative analyses of a control sample of known composition and a human fecal sample from varying amounts of input genomic DNA (1 ug, 200 ng, 5 ng), and present the corresponding library preparation workflows for standard, low input, and Ultra-Low methods. We demonstrate that the metagenome assembly, taxonomic assignment, and gene finding analyses are comparable across all methods for both samples, providing access to HiFi sequencing even for DNA-limited sample types.

Organization: PacBio, National Human Genome Research Institute, University of Chicago, Shoreline Biome, University of Warwick
Year: 2020

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