2. Data Trimming

Illumina data trimming

Also here, there are many options, e.g., Trimmomatic, fastp, and more fastp:

fastp --in1 file_1.fq.gz --in2 file_2.fq.gz --out1 illumina_1.fastq.gz --out2 illumina_2.fastq.gz --unpaired1 illumina_u.fastq.gz --unpaired2 illumina_u.fastq.gz

Trimmomatic:

java -jar trimmomatic-0.39.jar PE input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz

Oxford Nanopore data trimming

For this we will use here porechop. Sometimes it is necessary to join several fastq files into one:

cat fastq_runid_*.fastq.gz > porechop/all.fastq.gz
cd porechop
porechop -i all.fastq.gz -o porechop_all.fastq.gz --threads 10 > porechop.out