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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
261 stars 48 forks source link

Racon as a library #184

Open iqbal-lab opened 3 years ago

iqbal-lab commented 3 years ago

Hi there

Is there any way to call racon as a C++ library ? I can imagine situations where this would be super useful

rvaser commented 3 years ago

Hello Zamin, here it is: https://github.com/lbcb-sci/racon/tree/library. If you want to see an example how to integrate it check out de novo assembler https://github.com/lbcb-sci/raven. Just note that the library uses a minimap clone with parameters set for long reads, you cannot use your own overlaps (you only pass query/target sequences), and quality values of a FASTQ file are compressed block-wise. We will enable a more parameterized library version sometime in the future on the master branch.

Best regards, Robert

iqbal-lab commented 3 years ago

Thanks so much for this!!