Table 1. Profiling and miRNA assignment across 5 methods in 3 separate samples.

	Human Adipose Tissue (SRR772563)
Method	Processing time	miRNA Reads	miRNAs	miRNAs >10 RPM
miRge	26 sec	2,041,334	479	245
miRExpress 2.0	3.5 min	1,503,704	593	240
omiRAs	14 min	1,672,612	458	238
miRDeep2	13.5 min	1,969,122	432	189
sRNAbench	7 min	1,916,307	969	278
Chimira	2 min	2,044,664	804	268
UEA small RNA Workbench	3.6 min	1,583,013	578	225
	Human Beta Cell (SRR873410)
Method	Processing time	miRNA Reads	miRNAs	miRNAs >10 RPM
miRge	5.2 min	26,169,405	884	306
miRExpress 2.0	62 min	16,386,290	878	260
omiRAs	55 min	25,823,397	804	288
miRDeep2	39.5 min	19,949,196	489	196
sRNAbench	21 min	23,755,866	598	276
Chimira	24.4 min	26,238,680	1,499	323
UEA small RNA Workbench a
	Mouse Heart (SRR402445)
Method	Processing time	miRNA Reads	miRNAs	miRNAs >10 RPM
miRge	2.7 min	8,783,714	519	274
miRExpress 2.0	22.7 min	6,939,148	742	247
omiRAs	16 min	8,298,256	525	254
miRDeep2	13 min	6,336,341	529	216
sRNAbench	13 min	7,696,386	927	294
Chimira	10.2 min	8,839,153	893	265
UEA small RNA Workbench	9 min	4,497,946	583	226

Starting read counts: SRR772563 = 2,373,604 reads; SRR873410 = 33,233,648 reads; SRR9402445 = 15,981,680 reads. Each method was run with the number of processing cores reported: miRge—5 cores; miRExpress 2.0–5 cores; omiRAs—5 cores; miRDeep2–1 core; sRNAbench—unknown; Chimira—unknown; UEA small RNA Workbench—24 cores. Bold indicates fastest time and most miRNA reads.

^a unable to complete due to memory limitations.