TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing

Table 1 Datasets for evaluating all methods

Dataset	Sample	Type of barcode kit	Size of barcode kit	Barcode length (bp)	Number of reads
S-ET_ONT12	ETEC	ONT_EXP-NBD104	12	24	12,000
S-ET_ONT24	STEC	ONT_SQK-16S024	24	24	24,000
S-ET_ONT96	ETEC, STEC, and HS	ONT_EXP-PBC096	96	24	96,000
M-ESH_TD795	ETEC, STEC, and HS	Initially designed by TDFPS-Designer	795	20	795,000
M-ESH_TD1093	ETEC, STEC, and HS	Initially designed by TDFPS-Designer	1093	24	1,093,000
M-ESH_TD2120	ETEC, STEC, and HS	Initially designed by TDFPS-Designer	2120	30	2,120,000
L-ESH_TD137	ETEC, STEC, and HS	Finally designed by TDFPS-Designer	137	20	691,850
L-ESH_TD410	ETEC, STEC, and HS	Finally designed by TDFPS-Designer	410	24	2,070,500
L-ESH_TD1779	ETEC, STEC, and HS	Finally designed by TDFPS-Designer	1779	30	8,983,950

Here, the full name of ETEC is Enterotoxigenic Escherichia coli, the full name of STEC is Shiga toxin-producing Escherichia coli, and the full name of HC is Historical Shigella. For “ONT_EXP-NBD104,” “ONT” implies that it is designed by ONT, and “EXP-NBD10” is its kit name. “ONT_EXP-NBD104” and “ONT_SQK-16S024” imply the same meaning as “ONT_EXP-NBD104.” Specifically, L-ESH_TD137, L-ESH_TD410, and L-ESH_TD1779 include 1% negative samples that were not successfully barcoded. These negative samples serve as a “noise class”

ISSN: 1474-760X