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isovic / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116 Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
https://github.com/lbcb-sci/racon
MIT License
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error: overlap is not transmuted! #209

Open Saveli01 opened 2 years ago

Saveli01 commented 2 years ago

Hello, Thank you for writing this very useful program. I hope you can help me with this problem. I see other issues about this error but I haven't gotten it to work.

I ran minimap2 on reference.fasta and target.fasta.
minimap2 -a reference.fasta target.fasta > out.sam

Followed by racon: racon reference.fasta out.sam target.fasta

I also tried with minimap2 output in paf format. In each case I get an error: error: overlap is not transmuted!

Can you suggest how to fix this? Any advice will be appreciated.

rvaser commented 2 years ago

Hi, you misplaced the arguments in the Racon commands Please try the following:

minimap2 -a B.fa A.fa > out.sam
racon A.fa out.sam B.fa > out.racon.fa

Best regards, Robert

Saveli01 commented 2 years ago

Ah, thank you! To confirm, is the reference in your case A or B?

rvaser commented 2 years ago

A = reads B = reference

You can run racon --help to see the arguments (also minimap2 --help).

Saveli01 commented 2 years ago

Thanks again.
I appreciate your help.

Saveli01 commented 2 years ago

Asking for your advice again... My target sequence is: 2,117,597,479 (haploid) My reference sequence is: 5,596,238,300 (diploid) The racon output is: 657,072,055

The paf file (from minimap2) contains 2019406 unique contigs from the target (cut -f 1 | sort | uniq). But the target has 3678064 contigs, so about half couldn't be mapped, which is fine and not unexpected.

So, my plan is to take all the unmapped contigs from the target and append them to the racon consensus so nothing is lost. I wanted to ask your opinion on this in case I am not understanding this correctly.

rvaser commented 2 years ago

You can use option -u (--include-unpolished) in Racon to get all contigs back.

Saveli01 commented 2 years ago

Great!
Thanks again.