Racon output missing - Githubissues

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 output missing #124

Closed mradz19 closed 5 years ago

mradz19 commented 5 years ago

I'm new to using racon and have managed to get it working to polish a draft assembly with nanopore reads. However I caanot find the output file from racon, nothing is generated in the directory I run racon from.

Does racon output polished contigs in a different directory?

rvaser commented 5 years ago

Hi Michael, racon outputs polished sequences to stdout so you have to pipe your command to a file like bellow:

racon -t 12 reads.fasta overlaps.paf assembly.fasta > polished_assembly.fasta

Best regards, Robert

mradz19 commented 5 years ago

Hi @rvaser

Thanks for the prompt reply and the easy fix!