Fig. 1
From: fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data
a Performance testing of fastQ_brew. FASTQ formatted files containing different numbers of reads (110 MB [462,664 reads] to 4.5 GB [24,159,698 reads]) were provided as input to fastQ_brew and ran using default settings to return summary statistics for each dataset. b Relationship between nucleotide position and Phred quality score. fastQ_brew was used to determine the average Phred quality score from a FASTQ dataset comprising 462,664 reads after the length trimming methods was invoked to trim each read from position 1–20. A negative correlation between increasing nucleotide position and quality was observed. c The quality filter method within fastQ_brew was tested by plotting the Phred scores before (blue bars) and after (red bars) quality filtering. After filtering, there was a shift in the distribution of reads towards higher quality Phred values. d Execution speed for commonly used FASTQ filtering tools were compared with fastQ_brew. For all analyses, the same file and trimming task was applied. The following software were compared and presented: fastq_brew ver 1.0.2, trimmomatic ver 0.36, NGSQCToolkit ver 2.3.3, Prinseq ver 0.20.4, seqtk, Fastxtoolkit ver 0.0.13, ngsShoRT ver 2.2, BBDuk ver 37.22, and Cutadapt ver 1.9.1