Question: tools for global alignment
0
gravatar for genya35
4 weeks ago by
genya3510
genya3510 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 • 158 views
ADD COMMENTlink modified 4 weeks ago by h.mon23k • written 4 weeks ago by genya3510
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 4 weeks ago by jrj.healey10k
0
gravatar for h.mon
4 weeks ago by
h.mon23k
Brazil
h.mon23k 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 4 weeks ago by h.mon23k
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