About the low depth sequence assmble

lbcb-sci / GNNome

A framework for training graph neural networks to untangle assembly graphs obtained from OLC-based de novo genome assemblers.

BSD 3-Clause "New" or "Revised" License

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About the low depth sequence assmble #3

Closed ld9866 closed 7 months ago

ld9866 commented 7 months ago

Dear developer: I am trying to assemble the genome using about 15-20X nanopore data and about 15X illumina genome. The genome we are going to assemble , I would like to ask if this is feasible. I don't know if the software can meet this need? Best day!

lvrcek commented 7 months ago

Hi,

This tool does not support Illumina data, as it was implemented to work with long reads, mainly PacBio HiFi and Oxford Nanopore. For the 15-20X ONT data that you mention, you can try to first build the graph with Raven and do the decoding with GNNome. THe necessary steps are stated in README, but let me know if you will have any other questions.

ld9866 commented 7 months ago

Thank you!