TABLE 2.

Results of BUSCO analysis for various combinations of Nanopore and/or Illumina polishers.

Polisher (ONT reads)	Polisher (Illumina reads)	Rank	Complete, %	Complete	Fragmented	Missing	Single-copy	Duplicated
Medaka	Pilon-bt2 + POLCA	8	99.46	3139	5	11	3094	45
Medaka	Pilon-bt2	8	99.46	3139	5	12	3093	45
Medaka	Pilon-BWA	10	99.43	3138	6	12	3092	45
Medaka	POLCA	2	99.49	3140	5	11	3095	45
Medaka	POLCA X2	2	99.49	3140	5	11	3094	45
Medaka	–	14	98.42	3106	23	27	3061	45
Racon	–	18	93.44	2949	109	97	2912	37
Racon X2	Pilon-bt2 + POLCA	2	99.49	3140	5	11	3095	45
Racon X2	Pilon-bt2	12	99.33	3135	9	11	3091	45
Racon X2	Pilon-BWA	13	99.18	3130	12	14	3087	43
Racon X2	POLCA	2	99.49	3140	5	11	3095	45
Racon X2	POLCA X2	2	99.49	3140	5	11	3095	45
Racon X2	–	16	93.60	2954	107	96	2916	38
Racon X3	–	15	93.63	2955	108	93	2917	38
Racon X4	–	17	93.54	2952	110	94	2915	37
–	POLCA X2	10	99.43	3138	6	11	3094	44
–	–	19	88.53	2794	196	166	2760	34
MaSuRCa-CA hybrid assembly		1	99.56	3142	5	9	3083	59
MaSuRCa-Flye hybrid assembly		2	99.49	3140	6	10	3096	44

Rank, place in the overall ranking according to the number of complete (single-copy + duplicated) BUSCOs; ONT, Oxford Nanopore Technologies; bt2, bowtie2; X2, X3, X4, number of iterations; MaSuRCA-CA, MaSuRCA coupled with Celera Assembler; MaSuRCA-Flye, MaSuRCA coupled with Flye. The results are averaged across four assemblers: Canu (contigs and unitigs), Flye, Shasta, and wtdbg2.