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bowtie2

By Langmead B., Salzberg S., Last update 1494698999
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bowtie2 description

Bowtie2 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.


Parent program: bowtie

Bowtie2 is one of the most popular and efficient sequencing read aligners. It maps reads to a reference genome or other sequences and uses full-text minute index and Burrows-Wheeler transform. Moreover, it allows local, paired-end and gapped-read alignment unlike its predecessor Bowtie. Bowtie2 creates so-called FM index (a special data structure) to keep its memory footprint small. 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. For the human genome, its memory footprint is typically around 3.2 GB.