/home/linux/Plocha/TrimGalore-0.4.5/trim_galore --illumina --quality 20 --paired --length 100 /home/linux/Plocha/S1_L001_R1_001.fastq /home/linux/Plocha/S1_L001_R2_001.fastq

bwa index /home/linux/Plocha/Ref.fasta

bwa mem /home/linux/Plocha/Ref.fasta S1_L001_R1_001_val_1.fq S1_L001_R2_001_val_2.fq > /home/linux/Plocha/S1.sam

samtools view -F 4 -Sbh /home/linux/Plocha/S1.sam > /home/linux/Plocha/S1.bam

samtools sort /home/linux/Plocha/S1.bam > /home/linux/Plocha/S1_sorted.bam

samtools index /home/linux/Plocha/S1_sorted.bam

samtools depth -a /home/linux/Plocha/S1_sorted.bam > /home/linux/Plocha/S1.txt





