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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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How to create overlaps? #170

Closed bioramg closed 3 years ago

bioramg commented 3 years ago

Hi, I would like to use Racon for my ONT contigs. I am having ONT contigs output from Canu and Illumina reads. I extracted potential ONT contigs and would like polish using Illumina reads. But I could not understand what does mean by Overlaps file and how to create it? Thank you.

rvaser commented 3 years ago

Hi, you need to map all the reads to your contigs. For example with minimap2 run the following:

minimap -t <threads> -x sr canu_contigs.fasta illumina_reads.fastq > overlaps.paf

and afterwards run racon as below:

racon -t <threads> illumina_reads.fastq overlaps.paf canu_contigs.fasta > polished_canu_contigs.fasta

Best regards, Robert

bioramg commented 3 years ago

Dear Roberts, Thank you so much for your suggestions.

I would like to know is it possible to use Illumina read files as a separate files rather than combined reads?

Best regards, Raman. G

rvaser commented 3 years ago

Unfortunately no, you need to comine the paired end reads. There is a script here that does that for you.