Table 1.

Analysis of the influence of different threshold values on reference genome selection after taxonomy identification and compression ratios

Data	Original (MB)	Comp. (MB)	Processing time	Align. %	No. files	Comp. (MB)	Processing time	Align. %	No. files
ERR321482	1429	191	299 m 20 s	26.99	211	193	239 m 28 s	24.22	29
			422 m 21 s	3.57	1480		398 m 3 s	6.5	1567
			12 m 24 s				8 m 13 s
SRR359032	3981	319	127 m 34 s	57.72	26	320	93 m 60 s	57.71	7
			245 m 53 s	9.7	30		206 m 18 s	9.71	32
			8 m 37s				7 m 27 s
ERR532393	8230	948	639 m 55 s	45.78	267	963	522 m	42.45	39
			1061 m 50 s	1.98	1456		1067 m 49 s	7.16	1639
			73 m 59 s				28 m 13s
SRR1450398	5399	703	440 m 4 s	7.14	190	703	364 m 34 s	6.82	26
			866 m 56 s	0.6	793		790 m 52 s	0.91	818
			21 m 2 s				17 m 38 s
SRR062462	6478	137	217 m 21 s	2.55	278	139	197 m 15 s	2.13	50
			254 m 26 s	0.13	570		241 m 2 s	0.51	656
			15 m 45 s				19 m 31 s

Columns in bold represent a threshold of 75 species, while the columns not bolded correspond to a cutoff of 10 species. The results are shown for MetaCRAM-Huffman. “Align. %” refers to the alignment rates for the first and second round, and “No. files” refers to the number of reference genome files selected in the first and second iteration. Processing times are recorded row by row denoting real, user, and system time in order