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BenLangmead / bowtie2

A fast and sensitive gapped read aligner
GNU General Public License v3.0
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Feature request: only report the best alignment of one sequence #413

Open seahurt opened 1 year ago

seahurt commented 1 year ago

I am using bowtie2 for metagenomics analysis, and my index always contains many sequences.

When I using "-k 100", the output 100 aliment may only contains result of 30 or less sequences.

So I really wish bowtie2 will have a option to only report the best alignment of a sequence, like blastn's -subject_besthit