minimap2 -a /home/rezaeir/NanoporeData/ont-guppy/bin/17-05-2021-cas9-drunkCas9-combined/ref/HSV_US9_ref.fasta HSV-US9-Cas9-0.001.fastq.gz > HSV-US9-Cas9-0.001.sam

samtools view -S -b HSV-US9-Cas9-0.001.sam > HSV-US9-Cas9-0.001.bam

samtools view -b -F 4 HSV-US9-Cas9-0.001.bam > HSV-US9-Cas9-0.001.mapped.bam

samtools sort -@ 16 HSV-US9-Cas9-0.001.mapped.bam > HSV-US9-Cas9-0.001.mapped.sorted.bam

samtools index -@ 16 HSV-US9-Cas9-0.001.mapped.sorted.bam