canu polishing with CLR reads

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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canu polishing with CLR reads #208

Open botellaflotante opened 2 years ago

botellaflotante commented 2 years ago

Hello, I have a canu assembly with CLR reads (ca. 30X coverage). I used racon for polishing with the same reads... I got as a result much larger contigs. I don't have a reference genome to compare if what racon did I right as it seems based on contig lengths... Is this approach supposed to work well, or only illumina reads are recommended for improving this kind of assembly?

thanks

rvaser commented 2 years ago

Hello, it can happen that Racon extends a given assembly. Try to evaluate with BUSCO or if you have cdna data run paftools asmgene.

Best regards, Robert