# HD/TVM Genome Sequencing Course

- Align the reads with minimap2 -> SAM file
`minimap2 /mnt/.../reference.fasta /mnt/.../nanopore_fastq/*`
- Sort the samfile by position
`samtools sort -O BAM Sdl.sam >Sdl_sorted.bam`
- Make an index
`samtools index Sdl_sorted.bam`
- Copy the BAM file, its index, and the reference FASTA file to your computer
`scp [e-mail]:filename .` (on your Mac)
(or use CyberDuck or WinSCP)

In IGV
- Load the FASTA file as "genome file"
- Load the BAM file as "track file"