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basecalling

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Basecalls raw Oxford Nanopore signal (POD5/FAST5) into reads with Dorado, choosing the chemistry-matched model and accuracy tier (fast/hac/sup), requesting modified bases (5mCG_5hmCG, 6mA, m6A) at basecall time, and handling duplex, demultiplexing, trimming, and HERRO read correction. Covers why the model+version is an irreversible analysis decision, why methylation cannot be recovered later, and why downstream polish/variant models must match the basecaller. Use when converting POD5/FAST5 to reads, picking a Dorado model for R9/R10 or RNA004, enabling methylation calling, basecalling duplex, demultiplexing barcoded runs, or correcting reads for assembly.

When to use

• converting POD5/FAST5 to reads
• picking a Dorado model for R9/R10 or RNA004
• enabling methylation calling
• basecalling duplex
• demultiplexing barcoded runs
• correcting reads for assembly
• trimming adapters and primers
• aligning reads with minimap2

When not to use

• PacBio basecalling
• HiFi assembly

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