Question: tools for global alignment
0
gravatar for genya35
6 months ago by
genya3520
genya3520 wrote:

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 • 315 views
ADD COMMENTlink modified 6 months ago by h.mon26k • written 6 months ago by genya3520
1

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

That's not what global alignment does.

ADD REPLYlink written 6 months ago by jrj.healey13k
0
gravatar for h.mon
6 months ago by
h.mon26k
Brazil
h.mon26k wrote:

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.

ADD COMMENTlink written 6 months ago by h.mon26k
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