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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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Racon for consensus then error correcting #50

Closed jelber2 closed 6 years ago

jelber2 commented 6 years ago

Hi, Sorry to bother you again, but I have a question about Racon's suggested use. First, off I took a mammalian de novo assembly (Illumina short-insert [500bp] and long-insert [5kbp] reads) and filled in gaps with 10x coverage PacBio Sequel reads with PBJelly. Then I mapped the PacBio reads to the PBJelly assembly and created a consensus with Racon (using --bq -1). Now I would like to error correct the Racon assembly with the original Illumina short-insert reads used for the de novo assembly (will not include the mate-pair reads), but Pilon seems very slow for this purpose considering this is a 2Gbp genome [Right now we are trying to split up the genome into chunks to see how well that Pilon performs in that regard]. Does it seem reasonable to use minimap2 to overlap the Illumina short-insert reads into a PAF and then run Racon in error correct mode? Note that I am using commit 0834442ab980b10f7b0805570d1edab19d268767 on the master branch.

rvaser commented 6 years ago

Hello, today we will be releasing a new version of Racon which supports Illumina (with other stuff). And yes, you will be able to use 'minimap2 -x sr' with the new version, in both normal and error correction modes.

Best regards, Robert

rvaser commented 6 years ago

You can go ahead and try refactor_v branch :)

jelber2 commented 6 years ago

Should I rerun the PBJelly assembly through the updated version of Racon (i.e., create consensus with PacBio reads overlapping the PBJelly assembly)? Obviously, I don't need to redo the mapping of the PacBio reads to the assembly- rather redoing Racon step with newer version.

rvaser commented 6 years ago

I don't think it is necessary, the newer version is just faster and uses less memory. Map the Illumina reads on polished assembly and you are good to go (before polishing with illumina, you should have at least 1 iteration of consensus with 3rd gen data).

rvaser commented 6 years ago

New version is now on master branch.