PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm

BMC Bioinformatics

Table 1 Performance comparison of tested trimmers applied to two real life datasets.

	PEAT	AR^*	EA^*	TG^*	GATK^*	SeqPrep	TM^*
GSM929772 (sequence depth: 152.8M)
Time	1h 40m	36h 35m	3h 59m	4h 31m	14h 51m	22h 49m	12h 07m
# Trimmed	7,705,821	2,568,156	5,444,126	15,023,863	6,843,371	5,795,255	15,298,851
# Mappable	5,985,640	2,107,352	4,735,584	11,160,564	5,562,822	5,031,866	11,158,090
aTP	7,088,576	2,507,720	5,426,673	4,682,889	6,444,882	5,789,997	3,032,621
GSM929773 (sequence depth: 209.7M)
Time	1h32m	33h 30m	3h 40m	3h 54m	13h 55m	20h 07m	10h 51m
# Trimmed	10,587,748	3,243,421	8,659,761	17,427,938	10,191,334	9,070,298	22,184,570
# Mappable	8,791,108	2,708,858	7,604,812	13,991,491	8,755,726	7,981,609	17,451,029
aTP	10,317,323	3,177,176	8,535,723	7,535,502	10,063,241	9,062,206	5,046,115

^*Abbreviations: AR(AdapterRemovel); EA(ea-utils); TG(Trim_Galore); GATK (GATK ReadAdaptorTrimmer); TM(Trimmomatic)

ISSN: 1471-2105