Question: Command Line Tools To Do Long Sequence Alignment
0
gravatar for Xingyu Yang
5.7 years ago by
Xingyu Yang260
Atlanta
Xingyu Yang260 wrote:

Hi, Is there any software can perform large number of long sequence alignment? It's good to get a sam file.

I want to remap denovo assembled scaffolds/contigs to reference genome to identify structural variation.

alignment • 2.9k views
ADD COMMENTlink modified 5.6 years ago by Chris Fields2.1k • written 5.7 years ago by Xingyu Yang260
1
gravatar for Istvan Albert
5.6 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

LASTZ has been developed for this purpose:

http://www.bx.psu.edu/~rsharris/lastz/

ADD COMMENTlink written 5.6 years ago by Istvan Albert ♦♦ 81k
1
gravatar for Chris Fields
5.6 years ago by
Chris Fields2.1k
University of Illinois Urbana-Champaign
Chris Fields2.1k wrote:

bwa-mem can do long alignments and will generate SAM/BAM.  I have used this to align scaffolds up to 7.5M against a reference genome.

http://bio-bwa.sourceforge.net

ADD COMMENTlink written 5.6 years ago by Chris Fields2.1k
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