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I have assembled some genome from Sequel PacBio data both with HGAP4 on the SMRT Link interface and using canu on the command line. The HGAP4 assembler outputs a fastq file of the final assembly such that I can see how reliable the sequence is along the genome. On the other hand, canu does no such thing, which means I do not know how much I can trust each nucleotide in the assembly? Is there a way canu can output the fastq file as well or at least some depth information at each base?

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I've created an issue on the Canu github repository for this. I'm not aware of any existing functionality to output FASTQ files, but think that this would be a useful feature to have.

It would be possible to create something like this by aligning the original reads to the genome, generating a pileup from that alignment, then determining the sequence likelihood based on that pileup. Unfortunately, I don't have any scripts that I've written to do that... yet.

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