Question

Command Line Tools To Do Long Sequence Alignment

0

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10.6 years ago

Xingyu Yang ▴ 280

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 • 4.5k views

ADD COMMENT • link updated 3.2 years ago by Ram 44k • written 10.6 years ago by Xingyu Yang ▴ 280

Ram · Answer 1 · 2014-04-17

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10.6 years ago

Istvan Albert 101k

LASTZ has been developed for this purpose.

ADD COMMENT • link updated 3.2 years ago by Ram 44k • written 10.6 years ago by Istvan Albert 101k

Ram · Answer 2 · 2014-04-20

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10.6 years ago

Chris Fields ★ 2.2k

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.

ADD COMMENT • link updated 3.2 years ago by Ram 44k • written 10.6 years ago by Chris Fields ★ 2.2k