Please use this identifier to cite or link to this item: https://doi.org/10.1186/s12915-021-01141-x
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dc.titleONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone
dc.contributor.authorSrivathsan, Amrita
dc.contributor.authorLee, Leshon
dc.contributor.authorKatoh, Kazutaka
dc.contributor.authorHartop, Emily
dc.contributor.authorKutty, Sujatha Narayanan
dc.contributor.authorWong, Johnathan
dc.contributor.authorYeo, Darren
dc.contributor.authorMeier, Rudolf
dc.date.accessioned2022-10-11T07:46:01Z
dc.date.available2022-10-11T07:46:01Z
dc.date.issued2021-09-29
dc.identifier.citationSrivathsan, Amrita, Lee, Leshon, Katoh, Kazutaka, Hartop, Emily, Kutty, Sujatha Narayanan, Wong, Johnathan, Yeo, Darren, Meier, Rudolf (2021-09-29). ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone. BMC Biology 19 (1) : 217. ScholarBank@NUS Repository. https://doi.org/10.1186/s12915-021-01141-x
dc.identifier.issn1741-7007
dc.identifier.urihttps://scholarbank.nus.edu.sg/handle/10635/231912
dc.description.abstractBackground: DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity which are critical tasks at a time of rapid biodiversity loss. However, widespread adoption of barcodes requires cost-effective and simple barcoding methods. We here present a workflow that satisfies these conditions. It was developed via “innovation through subtraction” and thus requires minimal lab equipment, can be learned within days, reduces the barcode sequencing cost to < 10 cents, and allows fast turnaround from specimen to sequence by using the portable MinION sequencer. Results: We describe how tagged amplicons can be obtained and sequenced with the real-time MinION sequencer in many settings (field stations, biodiversity labs, citizen science labs, schools). We also provide amplicon coverage recommendations that are based on several runs of the latest generation of MinION flow cells (“R10.3”) which suggest that each run can generate barcodes for > 10,000 specimens. Next, we present a novel software, ONTbarcoder, which overcomes the bioinformatics challenges posed by MinION reads. The software is compatible with Windows 10, Macintosh, and Linux, has a graphical user interface (GUI), and can generate thousands of barcodes on a standard laptop within hours based on only two input files (FASTQ, demultiplexing file). We document that MinION barcodes are virtually identical to Sanger and Illumina barcodes for the same specimens (> 99.99%) and provide evidence that MinION flow cells and reads have improved rapidly since 2018. Conclusions: We propose that barcoding with MinION is the way forward for government agencies, universities, museums, and schools because it combines low consumable and capital cost with scalability. Small projects can use the flow cell dongle (“Flongle”) while large projects can rely on MinION flow cells that can be stopped and re-used after collecting sufficient data for a given project. © 2021, The Author(s).
dc.publisherBioMed Central Ltd
dc.rightsAttribution 4.0 International
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.sourceScopus OA2021
dc.subjectBiodiversity discovery
dc.subjectBioinformatics
dc.subjectCitizen science
dc.subjectDNA barcoding
dc.subjectMinION
dc.subjectOxford nanopore
dc.subjectSpecies delimitation
dc.typeArticle
dc.contributor.departmentDEPT OF BIOLOGICAL SCIENCES
dc.contributor.departmentTROPICAL MARINE SCIENCE INSTITUTE
dc.description.doi10.1186/s12915-021-01141-x
dc.description.sourcetitleBMC Biology
dc.description.volume19
dc.description.issue1
dc.description.page217
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