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Table 2 Summary of performance statistics for various trimming tools and number of reads

From: CIPHER: a flexible and extensive workflow platform for integrative next-generation sequencing data analysis and genomic regulatory element prediction

Tool Number of Reads Speed (sec) Adapters Remaining (%) False Positives (%)
BBDuk 1 M 1.2   
BBDuk 5 M 2.3 37.2 0.0099
BBDuk 10 M 3.5   
Cutadapt 1 M 208   
Cutadapt 5 M 1037 10.1 2.1059
Cutadapt 10 M 2084   
Trimmomatic 1 M 25   
Trimmomatic 5 M 93 57.7 0.0004
Trimmomatic 10 M 145   
  1. A table of performance tests and statistics between various trimming tools. Each tool was tested on datasets with 1 M, 5 M or 10 M reads. Speed tests were averaged across three replications. Adapters remaining and false positives tests were only conducted on 5 M read datasets, as the difference between 1 M, 5 M, and 10 M datasets was minimal