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Title: ONTbarcoder and MinION barcodes aid biodiversity discovery and identification by everyone, for everyone
Authors: Srivathsan, Amrita 
Lee, Leshon
Katoh, Kazutaka
Hartop, Emily
Kutty, Sujatha Narayanan 
Wong, Johnathan 
Yeo, Darren 
Meier, Rudolf 
Keywords: Biodiversity discovery
Citizen science
DNA barcoding
Oxford nanopore
Species delimitation
Issue Date: 29-Sep-2021
Publisher: BioMed Central Ltd
Citation: Srivathsan, 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.
Rights: Attribution 4.0 International
Abstract: Background: 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).
Source Title: BMC Biology
ISSN: 1741-7007
DOI: 10.1186/s12915-021-01141-x
Rights: Attribution 4.0 International
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