Recently I'm working on a de novo genome assembly project. Because the animal we study is so tiny, we had to pool DNA together from multiple individuals. And we've sequenced these DNA using both PacBio and Illumina. I've assemble the PacBio long reads into contigs, and want to do scaffolding and error correction using short reads. But I have the following two concern:
Can I use these short reads to correct the assembly? Since mixed DNA samples were used, how do the error correction tools discriminate "errors" or "individual difference"?
If I can do error correction, which one shoud be done first, error correction or scaffolding? I don't know what's the difference.
I have very little experience in this field. Sorry if the question is a bit basic. I'm totally stuck. Any help would be greatly appreciated.