bowtie2

ultrafast memory-efficient short read aligner

Install

All systems
curl cmd.cat/bowtie2.sh
Debian Debian
apt-get install bowtie2
Ubuntu
apt-get install bowtie2
image/svg+xml Kali Linux
apt-get install bowtie2
Windows (WSL2)
sudo apt-get update sudo apt-get install bowtie2
OS X
brew install bowtie2
Dockerfile
dockerfile.run/bowtie2

bowtie2

ultrafast memory-efficient short read aligner

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