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Command Line Tools To Do Long Sequence Alignment

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
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updated by Ram Ram • written by Xingyu Yang Xingyu Yang

2 answers

LASTZ has been developed for this purpose.

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updated by Ram Ram • written by Istvan Albert Istvan Albert

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.

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updated by Ram Ram • written by Chris Fields Chris Fields

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