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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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Different types of reads data to polish #175

Closed wjj666 closed 3 years ago

wjj666 commented 3 years ago

I want to use Illumina reads, Matepair reads, ONT reads and PacBio reads to polish assembly with Racon. Should I run racon four times with Illumina reads, Matepair reads, ONT reads and PacBio reads respectively? or use some specific parameter?

rvaser commented 3 years ago

Hi Lulu, you can combine ONT and Pacbio reads together in one file, and run two iterations of Racon. Afterwards, combine Illumina and Matepair reads together with https://github.com/isovic/racon/blob/master/scripts/racon_preprocess.py and run one iteration of Racon.

Best regards, Robert

wjj666 commented 3 years ago

How about the sam files? At the first iterations of Racon, the sam file is the alignments between ONT reads and contigs? At the second iterations of Racon, the sam file is the alignment between Pacbio reads and contigs?

rvaser commented 3 years ago

If you combine the reads in one file, the SAM files will contain both ONT and PB reads vs contigs in both iterations.