List the contents of the current working direcory
ls
change directory to move into the data folder
cd data/
unzip the gzipped FASTQ reads
gzip -d reads.R1.fq.gz
gzip -d reads.R1.fq.gz
print Breseq help menu
breseq -h
Run basic Breseq analysis with the provided reference genome and unzipped reads
breseq -j 16 -r genome.gbk reads.R1.fq reads.R2.fq