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tools for global alignment

Hello,

I would like to align fasta sequences size (40 to 400) bp to a reference about 290 bp globally. So if the sequence is smaller or larger than the reference it should not match. Which alignment tool do you recommend? I prefer to use bwa or bowtie but please suggest settings to use. I've used bwa mem under default settings and it aligned locally which is not what I'm looking for.

Thanks

alignment
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updated by h.mon h.mon • written by genya35 • genya35

So if the sequence is smaller or larger than the reference it should not match

That's not what global alignment does.

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written by Joe Joe

1 answer

Bowtie2 has an --end-to-end mode, read its manual. BBMap also is a global aligner.

But I agree with jrj.healey when he says you concept of global alignment is not correct.

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written by h.mon h.mon

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