Does SOAPnuke 2 not remove PCR duplications？

[MGI-tech-bioinformatics]

Dear Young,

I used SOAPnuke to filter NGS data, before using SOAPnuke, i used SOAPnuke 1.5.6 to remove PCR duplication by "-d", however i can't find "-d" or other parameters about PCR duplication.

Does SOAPnuke 2 not remove PCR duplications?

Thanks

huangshunkai@genomics.cn

[youngchan919]

Yes, we have removed the deduplication function since it might be more appropriate to be done in downstream analysis.
However, we would also like to know if there is any application scenario that it must be done in preprocessing stage.
If so, we will realize it in following version.