Bowtie 1.3.0 / Bowtie2 2.4.4 – Ultrafast Memory-efficient Short Read Aligner

Bowtie 1.3.0 / Bowtie2 2.4.4


Bowtie is an ultrafast, memory-efficient short read aligner. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds.


Bowtie 2 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.


the Center for Bioinformatics and Computational Biology




  • Linux / Windows /Mac OsX


Bowtie / Bowtie2



Langmead B, Trapnell C, Pop M, Salzberg SL.|
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Genome Biology 10:R25.

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