---
# System prepended metadata

title: HD/TVM Course

---

# HD/TVM Course

## Monday

- Log in to Linux server
- Look around with cd, ls, less etc.
- Inspect reference (FASTA) and reads (FASTQ)
- Run minimap2 on FASTQ to get SAM file
- Run samtools to sort and index SAM file
- Use IGV to look at alignment

##  Tuesday

- Revisit file types
- Revisit command line
- Install minimap2 and samtools on own computer
- Redo alignment on own computer

## Wednesday

- Basecalling
- QC, nanoplot

## Thursday

- Variant calling and interpretation

## Friday

- RNA-Seq