Skip to main content

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

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

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