Trimming with Trimmomatic

Fastq with adapter contamination

Trimming with the Trimmomatic tool

java -jar Trimmomatic-0.39/trimmomatic-0.39.jar \
    SE \
    -phred33 \
    -trimlog trimlog.txt \
    B_long_1_NNNGGTTNN_1.fastq.gz \
    trimmed.fastq \
    ILLUMINACLIP:Trimmomatic-0.39/adapters/TruSeq3-SE.fa:2:30:7 \
    MINLEN:15

Details of all the parameters can be found in the documentation on the Trimmomatic website.

Fastq after trimming