Question: Getting assembly from sam/bam file
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gravatar for priyanka.surana
11 days ago by
priyanka.surana0 wrote:

My assembly (asm.fa) is fragmented, so I align it against the reference (ref.fa). How can I use the sam output to get a new fasta file for my assembly, where the contigs are put together in scaffolds?

mininmap -ax asm5 ref.fa asm.fa > aln.sam

samtools sort aln.sam > aln.sorted.sam



Thank you and Best Regards,

Priyanka

alignment assembly • 69 views
ADD COMMENTlink modified 11 days ago by Philipp Bayer6.6k • written 11 days ago by priyanka.surana0
1
gravatar for Philipp Bayer
11 days ago by
Philipp Bayer6.6k
Australia/Perth/UWA
Philipp Bayer6.6k wrote:

I think it's probably best if you use RaGOO for that - https://github.com/malonge/RaGOO

It runs minimap2 using your contigs and a reference assembly and then orders the contigs based on the alignment. You may have to rerun your alignments, I don't know whether you can give it the sam file directly.

ADD COMMENTlink written 11 days ago by Philipp Bayer6.6k
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