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google / deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.
BSD 3-Clause "New" or "Revised" License
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pbccs parameters #7

Closed alexcorm closed 3 years ago

alexcorm commented 3 years ago

Hello,

In the online methods, you indicate that you didn't apply any filtering based on read quality for the CCS reads, and reads of qualities were included in the training dataset from pbccs output. Can you indicate the exact command line you used to generate ccs file?

Regards, Alex

armintoepfer commented 3 years ago

Hey Alex,

--all is sufficient.

Armin

danielecook commented 3 years ago

Yep - we used --all with ccs.