CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data

BMC Genomics

Table 2 Comparison of different tools in miRNA detection

	CAP-miRSeq	omiRAS	miRTools2	Novoalign
Version	v1.1	12/2013	v2	2.07.13
Aligner	Bowtie	Bowtie	SOAP	Novoalign⁺
Ref Genome	hg19	hg19	hg19	hg19
Time	5 hrs	12 hrs	Variable	6 hrs
Memory	4 GB	-	-	10 G
Mature miRNA (> = 2)	860	739	172	881
Novel miRNA	194	NA*	35	No prediction
Correlation with other tools	-	0.99	0.81	0.95

*NA–omiRAS requires at least two samples to run with differential expression analysis; however, it does not report novel miRNAs for each individual sample. ⁺Novoalign is just an alignment toot and it does not perform miRNA prediction and quantification. omiRAS and miRTool2 are web based tools and no memory usage information is available.

ISSN: 1471-2164