Align reads to the genome

First, use bowtie2 to align the sequencing reads in reads.fq to the reference genome using the index located at $REF; the reads are single-ended.

Output the results to the file aligned.sam, then sort the SAM file to output aligned.bam. Complete the following exercises before moving on to the next step:

• File aligned.sam contains reads mapped to the genome using bowtie2
• File aligned.bam is a sorted BAM file version of aligned.sam