Table 2.

Quality assessment of barcodes generated by ONTbarcoder at 200X read coverage (Consensus by Length) and 100X coverage (Consensus by Similarity). The accuracy of MinION barcodes is compared with the barcodes obtained for the same specimens using Illumina/Sanger sequencing. Errors are defined as the sum of substitution or indel errors. Denominators are the total number of nucleotides assessed

Dataset	No. of comparison barcodes	No. of barcodes with errors/No. of errors/% identity	# of Ns/%Ns
R10.3: Mixed Diptera: Sanger barcodes available	476	2/10/99.997%	19 (0.006%)
R10.3: Afrotropical Phoridae: Illumina barcodes availablea	3316	23/48/99.995%	284 (0.011%)
Flongle-Mixed Diptera Subsample: Sanger barcodes available	231	5/8/99.994%	91 (0.058%)

^a5 barcodes with very high distances from reference were excluded for R10.3: Afrotropical Phoridae dataset as they likely represent lab contamination (see Srivathsan, Hartop et al. [35])