Keep quality score when correcting with Canu assembler?

Question

[lizgzara]

I am using Canu assembler to do a de novo assembly of PacBio data. I noticed that when I corrected my reads it produced a .fasta not a .fastq file, therefore loosing the quality score data of my original raw PacBio reads. Is there any parameter or option I can add so that the quality score is not lost when issuing the "canu -correct" command? Thank you!

P.S. I am trying to pipe the corrected reads to MIRA and MIRA requires quality scores when I run it on Geneious.

Answer 1

[Rohit]

There is a chance to create dummy fastq files with desired quality, check out this post

BioPython: convert fasta to fastq without quality score input file

You can also use pbh5tools for this purpose.

[lizgzara]

Thank you! I ended up using Matt Shirley's code (from the link you provided) on the command line and it worked great!