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Bioinformatics Toolbox Interface for Bowtie Aligner

Bowtie aligns short DNA sequences to a reference genome.


Updated 18 Mar 2020

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).

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MATLAB Release Compatibility
Created with R2018a
Compatible with R2018a to R2020a
Platform Compatibility
Windows macOS Linux