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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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Multiple rounds of polishing #160

Closed 000generic closed 3 years ago

000generic commented 4 years ago

Given TGS and SGS reads, I've read in some of the issues that multiple rounds of TGS polishing followed by multiple rounds of SGS polishing is being used. Is this generally recommended? If so, I was wondering:

1) Should reads be remapped in between each round of polishing?

2) What methods or software are recommended or commonly used for evaluating and comparing (sequentially) polished transcriptomes?

I was initially going to do Racon TGS -> Racon SGS -> Pilon SGS but can try including multiple rounds at the Racon steps, if its generally thought to improve things.

rvaser commented 4 years ago

Hello Eric, your intended approach should suffice, there is no need for more iterations when you have SGS data. In case of multiple iterations with the same dataset, you need to remap between each round of polishing. I am unaware of any methods for sequential polishing and evaluation of transcriptomes. Also, I am not sure if Racon will work properly on transcripts due to alternative splicing.

Best regards, Robert

000generic commented 4 years ago

Hi Robert,

Great! Thank you for all the details.

Eric