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.

Jiang et al.

Jiang et al. BMC Bioinformatics 2014 15:182   doi:10.1186/1471-2105-15-182

Open Data