Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

BMC Bioinformatics

Table 2 Performance of adapter trimmers on 2Gbp simulated data

Method (Single End/Paired End)		Speed (Mbp/s)	Memory (Mb)	PPV (%)	Sen. (%)	Spec. (%)	mCC
FastX	SE	0.92	13.8	68.90	90.84	77.97	0.6683
SeqTrim	SE	0.03	115.7	67.07	85.27	81.24	0.6618
TagCleaner	SE	0.54	37.6	100.0	45.50	100.0	0.5898
EA-Tools	SE	12.04	17.7	59.24	99.72	61.32	0.6010
	PE	11.54	30.0	59.16	99.43	61.36	0.5983
Cutadapt	SE	4.36	34.5	94.55	96.27	96.93	0.9286
	PE	3.44	42.8	94.55	96.00	96.93	0.9266
TrimGalore	SE	3.81	19.4	59.24	99.72	61.32	0.6010
	PE	3.26	19.6	59.16	99.44	61.36	0.5984
SeqPrep	PE	0.64	22.0	99.84	99.82	99.92	0.9975
Btrim	SE	23.63	11.2	99.96	53.44	100.0	0.6503
	PE	5.79	15.3	99.89	53.30	100.0	0.6490
Scythe	SE	3.15	11.2	99.56	90.86	99.92	0.9283
Flexbar	SE	2.82	9.5	57.90	99.12	59.48	0.5814
	PE	2.70	9.7	57.77	99.09	59.29	0.5795
Trimmomatic	SE	16.73	2593.0	99.99	72.31	100.0	0.7907
	PE	16.40	2292.0	100.0	71.54	100.0	0.7850
AdapterRemoval	SE	1.67	6.3	75.09	97.74	81.89	0.7675
	PE	0.73	8.3	99.93	94.47	99.97	0.9566
AlienTrimmer	SE	1.64	2319.9	85.62	57.11	99.96	0.6769
	PE	1.61	2248.9	83.71	55.67	99.95	0.6659
Skewer	SE	8.79	13.6	94.56	96.32	96.93	0.9291
	PE	8.88	22.2	100.0	99.86	100.0	0.9989

Methods that process only single-end (SE) or paired-end (PE) reads are indicated.

ISSN: 1471-2105