44    ◾    Bioinformatics

java -jar ../Trimmomatic-0.39/trimmomatic-0.39.jar \

PE SRR957824_1.fastq SRR957824_2.fastq \

out_PE_SRR957824_1.fastq out_UPE_SRR957824_1.fastq \

out_PE_SRR957824_2.fastq out_UPE_SRR957824_2.fastq \

ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True \

LEADING:3 \

TRAILING:3 \

ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 \

SLIDINGWINDOW:5:30 \

MINLEN:150

fastqc out_PE_SRR957824_1.fastq out_PE_SRR957824_2.fastq

firefox out_PE_SRR957824_1_fastqc.html out_PE_SRR957824_2_fastqc.

html

Check out the reports of the two paired-end FASTQ files to see that only the reads with

equal length are left.

There are several other programs that can be used, as well, for the quality improvement

of FASTQ reads. For instance, Fastp can be used for the filtering of low-quality reads and

FIGURE 1.36  Trimmomatic processed forward FASTQ file.