Merging PacBio and Nanopore reads

Question

[Sbrillo]

Hi to every one,

I'm running a pipeline in which i need as an input file Pacbio reads but unfortunately the pacbio reads available have a low coverage (around 7 that is 3 unit below the minimun accepted from the pipeline). Since in my lab they are doing some Nanopore sequencing I was thinking if after the fastq file correction ( i always used canu) i can merge corrected nanopore and Pacbio reads in the same file (using cat for instance).

This will increase a lot the power of my analysis.

Do you know if that is possible?

Answer 1

[harishk0201]

You can absolutely merge the two technologies, but the profiling of errors used for the correction and trimming will be based on the more error-prone chemistry as the baseline.

Ref: https://github.com/marbl/canu/issues/1892