Hi Yue, sorry for the late reply. I have not yet tried precompiling the header and I am not sure how it would work at all with strongly templatized code → how would the compiler know which instantiations you actually use later on? Although other sources claim its possible: https://bytes.com/topic/net/answers/438738-should-templates-included-pch-files Do other people have experience with this? Something else you can do to speed up the build with SeqAn when using gcc is passing -flto=N where N is the number of your cores, possibly +1. This parallelizes most parts of the build even for a single translation unit. Best regards, -- Hannes Hauswedell PhD student Max Planck Institute for Molecular Genetics / Freie Universität Berlin address Institut für Informatik Takustraße 9 Room 019 14195 Berlin telephone +49 (0)30 838-75241 fax +49 (0)30 838-75218 e-mail hannes.hauswedell@[molgen.mpg.de|fu-berlin.de]