tools for global alignment

Question

[genya35]

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

[Joe]

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

That's not what global alignment does.

Answer 1

[h.mon]

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.