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lbcb-sci / raven

De novo genome assembler for long uncorrected reads
MIT License
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What are the other steps we should follow after raven assembly? #61

Closed thulasis closed 2 years ago

thulasis commented 2 years ago

Hi I am using nanopore data for assembly. It is rapid and computationally stable. Do you recommend other polishing methods like medaka after raven? I am getting some single contigs for genome assemblies but unable to circularize the genome. Do you suggest anything to solve this issue? I am using latest 1.8.1 version.

Is it possible to run raven with reference genome?

Thanks in advance, Tulasi

rvaser commented 2 years ago

Hi Tulasi, you can run medaka to polish the assembly further. For circularization you can try https://github.com/sanger-pathogens/circlator. For reference based assembly you can try https://github.com/rrwick/Rebaler.

Best regards, Robert

thulasis commented 2 years ago

Hi Tulasi, you can run medaka to polish the assembly further. For circularization you can try https://github.com/sanger-pathogens/circlator. For reference based assembly you can try https://github.com/rrwick/Rebaler.

Best regards, Robert

Hi Robert,

Thank you for your suggestion. I did some k-mer optimizations while running the rave and finally got the circular genome maps. I will definitely look at the rebaler for the reference based assembly. I will use medaka for the polishing.

Thanks again.

Best, Tulasi