bowtie2 binary package in Ubuntu Xenial amd64

 is an ultrafast and memory-efficient tool for aligning sequencing reads
 to long reference sequences. It is particularly good at aligning reads
 of about 50 up to 100s or 1,000s of characters, and particularly good
 at aligning to relatively long (e.g. mammalian) genomes.
 .
 Bowtie 2 indexes the genome with an FM Index to keep its memory footprint
 small: for the human genome, its memory footprint is typically
 around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes

Source package