Hello I was asked to perform an assembly polishment with Racon . The issue is that we are trying to assembly the genome of n algal specie . we have pacbio reads and illuima reads from the same sequencing library.
On my a pipeline fot that porpuse (after cleaing reads) can be this:
1) assembly the pacBio reads using Canu: https://genome.cshlp.org/content/27/5/722.short
2) mapping illumina reads against the produced contigs on step 1.
3) using a polisher like racon where input reads are illumina reads, input sam are the illuma reads against the conigs produced by pacbio reads and the fasta file with the assembled contigs (produced by pacbio)
is this a good strategy or the default pipeline ahead to polishing basecall errores produced by pacbio technologies?
Thanks for your time :)
