TABLE 1.

Publications using Oxford Nanopore Technologies sequencing data for Mycobacterium tuberculosis^a

First author	Year	Ref	WGS or targeted	Type of strain, cultured isolate or specimen	N	Sample preparation details and library preparation kit	Device	Flow cell used	Base-calling	Bioinformatic analysis	Main study aim	Main study findings
Eckert	2016	22	WGS	Laboratory (Mtb H37Rv), culture isolate	1	Biotinylated RNA bait enrichment, SQK-MAP003 or SQK-MAP004	MinION	Not listed	Metrichor 2D	MinKNOW, poretools, BLASR, LAST	Evaluate an adapted DNA enrichment protocol for MinION sequencing	DNA enrichment resulted in partial Mtb genome coverage
				Clinical, cultured isolate	1
Bainomugisa	2018	21	WGS	Clinical, cultured isolate	1	SQK-LSK108	MinION	R9.4	Albacore	MinKNOW, Nanopolish, Racon, Pilon, MUMmer, Canu, Circulator	Use NS plus short-read sequencing to assemble the XDR Mtb genome	Identification of known and novel genomic variants
Smith	2020	23	WGS	Clinical, cultured isolates	431	SQK-LSK109	MinION	R9.4	Guppy with FlipFlop Fast algorithm	QCAT, Minimap2, BWA mem, SAMTools, Kraken	Assess ONT sequencing for species identification, in silico spoligotyping, resistance prediction and phylogenetics	Performance and cost of ONT is comparable, to Illumina for genotyping and detection of resistance
Cervantes	2020	8	WGS	Laboratory (Mtb HN878), cultured isolate	1	Rapid Sequencing Kit	MinION	R9.4	Albacore	EPI2ME, What’s In My Pot, antimicrobial resistance mapping application	Evaluate ONT for WGS for drug resistance prediction from cultured and uncultured Mtb	no. of Mtb reads varied considerably and was very low for 2 when DNA was extracted directly from sputum
				Clinical, 4 cultured isolates, 2 specimens	6
George	2020	12	WGS	Laboratory (M. bovis BCG), cultured isolate (used to spiked sputum)	1	SQK-LSK109	GridION	R9.4	Guppy	Porechop, Centrifuge, in-house CRuMPIT workflow, Minimap2, SAMTools, Pysam	Develop an undemanding, cost-effective method for sequencing Mtb directly from clinical specimens	Use of a low-cost thermo-protection buffer and a single flow cell per sample resulted in sufficient Mtb genome coverage
				Clinical, specimens	20
Tafess	2020	24	Targeted	Clinical, cultured isolates	163	PCR amplification of 19 loci, SQK-LSK108	MinION	R9.4	Albacore	BacterioChek-TB, BWA	Develop targeted sequencing for Illumina MiSeq and ONT for prediction of resistance.	100% concordance between ONT and Illumina when low frequency variants are excluded
Chan	2020	25	Targeted	Clinical, specimens	12	PCR amplification of 10 loci, Ligation Sequencing 1D kit	MinION	R9	MinKNOW	Porechop, Minimap2, Nanopolish, Qualimap	Develop targeted sequencing workflows for Illumina MiSeq and ONT for prediction of resistance	95% concordance between ONT and Illumina for fixed variants
Cabibbe	2020	11	Targeted	Clinical, specimens	104	Deeplex Myc-TB PCR amplification, SQK-LSK108	MinION	R9.4	Albacore	Guppy, Porechop, Minimap2, SAMTools, VarScan2, NanoPack, AlignQC, Qualimap2	To evaluate the compatibility of Deeplex Myc-TB, with ONT MinION.	ONT MinION and Illumina MiniSeq results were fully concordant for drug resistance prediction.

^aN refers to the number of sequenced samples. Twenty replicates of one sample. Abbreviations: WGS, whole-genome sequencing; BCG, Bacillus Calmette-Guérin; ONT, Oxford Nanopore Technologies; XDR, extensively drug resistant; Mtb, Mycobacterium tuberculosis.