Racon polishing after Canu

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Hello Everyone,

I want to run Racon on Canu output files. It is my first time running this pipeline, hence I have a few basic questions:

  • For Racon’s “Overlap” field, which file of Canu should be used?
  • I see that all outputs of Canu are in fasta format. But Racon needs the input format in MHAP/PAF/SAM for “Overlap” field. Do I need to change the file format? If yes, which format should I use?

Thanks :smiley:

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Hi @SShivani22,
Racon requires to be provided with the mapping of the reads to the assembly generated by Canu. You can generate it by using minimap2.

Regards

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Thank you :smiley: I got the results :smiley: