[wgs-assembler-users] Trimming, Overlapping Paired Reads and WGS

[Corey W. <cor...@gm...>]

Hello,

I have two questions relating to one assembly I am working on.

- Should mate pair libraries be trimmed? Link to tech note on Illumina Mate
Pairs (pdf).
<http://www.illumina.com/documents/products/technotes/technote_nextera_matepair_data_processing.pdf>

At the moment I trim my Illumina Mate Pair reads using skewer
<https://github.com/relipmoc/skewer>. Since I can tell WGS the insert size,
orientation I imagine the overlapper would work just fine with getting
untrimmed reads.

- In the same vein; does WGS understand overlapped paired-end (aka
sloptigs)? For example if we sequence a 500bp insert with 300 cycles we
theoretically get 100bp overlap.

Thanks,

-Corey Wischmeyer