Hi All,

I was wondering how important is to get rid of exact duplicate Illumina reads before -- 

 1. Before using it for correcting PacBio reads (planning to use ProovRead)
 2. Before using it to polish a Pac-Bio only assembly using Pilon (Assembly was done using uncorrected PacBio reads - miniasm)
 3. 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!
It's not a good idea to remove duplicate reads unless your libraries are amplified.  If they *are* amplified, and you have reads appearing 10+ times, I highly recommend you change to an unamplified protocol, because you are wasting sequence.  And by duplicates, I mean that both read 1 and read 2 of pairs are duplicates...  otherwise the pairs are not, in fact, duplicates.

But - if you have a situation in which you are using an amplified library, and duplicate pairs occur, I recommend eliminating all duplicates and replacing them with a single copy of their consensus, in any situation other than quantification (e.g. RNA-seq).
