1. The sequencing reads

The reads have been preloaded to your working directory. Try ls reads.fq and head -n 8 reads.fq (why did we pick a multiple of 4 in our head command?).

2. The reference genome

In the following steps, you’ll map those reads to the Lambda phage reference genome.

We preloaded the bowtie2 indexes for that reference genome; its location is stored in the variable $REF. Use echo $REF to see the location.

For variant calling, you’ll also need the reference genome’s FASTA file, and its location is stored in the variable $REF_FASTA. Use echo $REF_FASTA to see the location (or use env to list all variables).