Question: Aligning fasta sequences against a reference genome with scaffolds
0
gravatar for thjnant
3.7 years ago by
thjnant80
Germany
thjnant80 wrote:

Hello,

I have a reference genome that consists only of scaffolds without the assignment of scaffolds to any chromosome. My reference genome is in fasta format.

I would like to extract those sequences that possibly belong to chromosome number 5 of my species. For that, I have a transcriptome de novo assembly from which I have obtained a list of fasta sequences that belong to chromosome 5.

What I would like to do now is to align my fasta sequences beloning to chromosome 5 obtained from transcriptome assembly against the reference genome scaffolds to obtain those scaffolds that belong to chromosome number 5.

My question is that what the best software is for this purpose?

Thank you very much for your help in n advance.

alignment • 2.2k views
ADD COMMENTlink modified 3.7 years ago by Istvan Albert ♦♦ 76k • written 3.7 years ago by thjnant80
0
gravatar for Istvan Albert
3.7 years ago by
Istvan Albert ♦♦ 76k
University Park, USA
Istvan Albert ♦♦ 76k wrote:

There are many good choices among them I'd recommend lastal or lastz ...

Note: despite the similar names the tools are completely unrelated 

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Istvan Albert ♦♦ 76k
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