Data from: A MinION™‐based pipeline for fast and cost‐effective DNA barcoding

DNA barcodes are useful for species discovery and species identification,
but obtaining barcodes currently requires a well-equipped molecular
laboratory, is time-consuming, and/or expensive. We here address these
issues by developing a barcoding pipeline for Oxford Nanopore MinION™ and
demonstrate that one flowcell can generate barcodes for ~500 specimens
despite high base-call error rates of MinION™ reads. The pipeline
overcomes the errors by first summarizing all reads for the same tagged
amplicon as a consensus barcode. Consensus barcodes are overall
mismatch-free but retain indel errors that are concentrated in
homopolymeric regions. They are addressed with an optional error
correction pipeline that uses conserved amino-acid motifs from publicly
available barcodes to correct the indel errors. The effectiveness of this
pipeline is documented by analysing reads from three MinION™ runs that
represent different stages of MinION™ development. They generated data for
(1) 511 specimens of a mixed Diptera sample, (2) 575 specimens of ants,
and (3) 50 specimens of Chironomidae. The run based on the latest
chemistry yielded MinION barcodes for 490 of the 511 specimens which were
assessed against reference Sanger barcodes (N=471). Overall, the MinION
barcodes have an accuracy of 99.3%-100% and the number of post-correction
ambiguities ranges from <0.01-1.5% depending on which correction
pipeline is used. We demonstrate that it requires ~2 hours of sequencing
to gather all information needed for obtaining reliable barcodes for most
specimens (>90%). We estimate that up to 1000 barcodes can be
generated in one flowcell and that the cost per barcode can be