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google / deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.
BSD 3-Clause "New" or "Revised" License
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Nanopore model availability #12

Closed ChangqingW closed 3 months ago

ChangqingW commented 5 months ago

I wonder if there are plans for training DeepSomatic for Nanopore samples anytime soon? If not, would you expect the performance to deteriorate greatly if I were to select the PacBio model for our Nanopore RNA-seq samples?

kishwarshafin commented 5 months ago

Hi @ChangqingW ,

Currently we do not have a ONT model publicly available with the release and we do not expect the pacbio model to work for nanopore. Can you please reach us by sending an email to shafin@google.com so we can assist you further?

kishwarshafin commented 3 months ago

Handled in email.