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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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no subreads available #45

Closed michaelabrouk closed 2 years ago

michaelabrouk commented 2 years ago

Hi,

I am working with sequencing output coming from Sequel IIe meaning that I only have the ccs.bam files available and not the subreads.bam. Is DeepConsensus can work without the alignment of subreads to ccs using actc in the preliminary step?

Thanks

armintoepfer commented 2 years ago

DeepConsensus requires subreads, which are not available when using Sequel IIe HiFi output.

michaelabrouk commented 2 years ago

Thank you for your answer.