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BenLangmead / bowtie2

A fast and sensitive gapped read aligner
GNU General Public License v3.0
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The optimized read length for bowtie2 to handle #383

Closed Duannai closed 7 months ago

Duannai commented 2 years ago

Hello, just an easy question.

What is the optimized read length for bowtie2 to handle? Can bowtie2 handle the reads shorter than 50 bp? For instance, the reads with 30 bp.

Thanks in advance!

Mort

ch4rr0 commented 2 years ago

Hello,

Bowtie is best suited for aligning short reads. Bowtie 2 can handle short reads, but you may need to tweak a few parameters, such as seed length (-L), if the desired alignments are not reported. I hope this helps.