<p>I've created an <a href="https://github.com/marbl/canu/issues/744" rel="nofollow noreferrer">issue</a> 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.</p>

<p>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.</p>

CC BY-SA 3.0
2017-12-28T02:05:26.477Z
2017-12-28T02:05:26.477Z
gringer
<p>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?</p>

<genome><assembly><fastq><genome-sequencing><canu>
Can the canu assembler output a fastq file of the final assembly just like HGAP4?
# Can the canu assembler output a fastq file of the final assembly just like HGAP4?

(Asked by: username_0 on 2017-12-28)

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?

**Tags:** genome, assembly, fastq, genome-sequencing, canu

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## 1 answers

### Answer by username_1 on 2017-12-28. Score: 2 | Accepted answer

I've created an [issue](https://github.com/marbl/canu/issues/744) 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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