I was wondering how important is to get rid of exact duplicate Illumina reads before --
- Before using it for correcting PacBio reads (planning to use ProovRead)
- Before using it to polish a Pac-Bio only assembly using Pilon (Assembly was done using uncorrected PacBio reads - miniasm)
- Before using the reads to do a hybrid de-novo-assembly using PBcR
Some of my Illumina libraries have significant amounts of reads duplicated >10 times. What are your recommendations to handle these duplicate reads considering the scenarios mentioned above?
Many thanks in advance!