Scientific article
Open access

Identifying microbial species by single-molecule DNA optical mapping and resampling statistics

Published inNAR Genomics and Bioinformatics, vol. 2, no. 1
Publication date2020

Single-molecule DNA mapping has the potential to serve as a powerful complement to high-throughput sequencing in metagenomic analysis. Offering longer read lengths and forgoing the need for complex library preparation and amplification, mapping stands to provide an unbiased view into the composition of complex viromes and/or microbiomes. To fully enable mapping-based metagenomics, sensitivity and specificity of DNA map analysis and identification need to be improved. Using detailed simulations and experimental data, we first demonstrate how fluorescence imaging of surface stretched, sequence specifically labeled DNA fragments can yield highly sensitive identification of targets. Second, a new analysis technique is introduced to increase specificity of the analysis, allowing even closely related species to be resolved. Third, we show how an increase in resolution improves sensitivity. Finally, we demonstrate that these methods are capable of identifying species with long genomes such as bacteria with high sensitivity.

  • European Commission - Horizon 2020 Framework Programme of the European Union called ADgut [686271];
  • European Commission - ERC Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement [751121]; ‘Agentschap Innoveren & Ondernemen' in the framework of an innovation mandate [HBC.2016.0246]; European Union Research Council through the ERC-2017-PoC Metamapper [768826];
Citation (ISO format)
BOUWENS, Arno et al. Identifying microbial species by single-molecule DNA optical mapping and resampling statistics. In: NAR Genomics and Bioinformatics, 2020, vol. 2, n° 1. doi: 10.1093/nargab/lqz007
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ISSN of the journal2631-9268

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