Bowtie 2 comes with some example files to get you started. The example files are not scientifically significant; we use the Lambda phage reference genome simply because it’s short, and the reads were generated by a computer program, not a sequencer. However, these files will let you start running Bowtie 2 and downstream tools right away.
Type in the command line to see the two sample FASTQ files.
We preloaded the Lambda phage reference genome into your sandbox, and stored the path in the variable $REF for convenience:
You can find pre-built Bowtie2 indexes for many genomes at benlangmead.github.io/aws-indexes.