Assessing Illumina, Nanopore and PacBio sequencing platforms at recovering high quality genomes from complex microbial communities

Mantas Sereika, Rasmus Hansen Kirkegaard, Emil Aarre Sørensen, Søren Michael Karst, Thomas Yssing Michaelsen, Mads Albertsen

Research output: Contribution to conference without publisher/journalPosterCommunication

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Abstract

Cheap short-read DNA sequencing has led to a massive increase of genome reference databases, although many genome drafts from environmental systems are highly fragmented due to strain heterogeneity, micro-diversity, and repeats that cannot be resolved with short reads. This poses an issue, as the absence of genes in incomplete and fragmented genomes fails to provide important genomic information about microbial species. Here, we show that combining short reads (Illumina) with Nanopore R9 sequencing of anaerobic digester sludge enables to acquire vastly greater numbers of more complete, high quality metagenome assembled genomes, compared to a short-read-only approach (86 vs 8 high quality genome drafts). We found PacBio circular consensus sequencing to also be an effective platform for genome-centric metagenomics (74 high quality drafts), albeit at higher costs per genome draft, compared to the hybrid Illumina-Nanopore approach (59.7 vs 23.4 $ per high quality draft).
Original languageEnglish
Publication date15 Nov 2021
Publication statusPublished - 15 Nov 2021
EventDanish Microbiological Society congress 2021 - Marmorhallen, Frederiksberg, Copenhagen, Denmark
Duration: 15 Nov 202115 Nov 2021
https://dms.dk/congress

Conference

ConferenceDanish Microbiological Society congress 2021
LocationMarmorhallen, Frederiksberg
Country/TerritoryDenmark
CityCopenhagen
Period15/11/202115/11/2021
Internet address

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