Skip to main content

Advertisement

Table 2 Performance of adapter trimmers on 2Gbp simulated data

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

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