/home/linux/Plocha/ART/art_bin_MountRainier/art_illumina -ss MSv1 -sam -i /home/linux/Plocha/Sim_1.fasta -p -l 150 -f 150 -m 500 -s 150 -o paired_dat

bwa index /home/linux/Plocha/Sim_1_ref.fasta

bwa mem /home/linux/Plocha/Sim_1_ref.fasta paired_dat1.fq paired_dat2.fq > /home/linux/Plocha/Sim_1.sam

samtools view -F 4 -Sbh /home/linux/Plocha/Sim_1.sam > /home/linux/Plocha/Sim_1.bam

samtools sort /home/linux/Plocha/Sim_1.bam > /home/linux/Plocha/Sim_1_sorted.bam

samtools index /home/linux/Plocha/Sim_1_sorted.bam

samtools depth -a /home/linux/Plocha/Sim_1_sorted.bam > /home/linux/Plocha/Sim_1.txt






