Tools for quality trimming at 5 prime? I'm looking for a tool that is capable to do quality trimming at 5' end and it is configurable. For example, I can choose the quality trheshold, the read length, etc. Any recommendations? 

I'm currently using sickle for quality trimming. However, one of my samples have very low quality at the beginning as well and sickle doesn't seem to be able to deal well with it.
You can have a look at cutadapt. It is capable of quality trimming for both ends as you can read here.