I've been using Trimmomatic by using LEADING, TRAILING and SLIDING WINDOW parameters. Recently we have seen that ILLUMINACLIP parameter is also being used mostly. Until we have seen this, we have been thinking that Trimmomatic is built to trim Illumina adapters specifically, therefore it would detect Illumina adapters and trim them automatically. But there is nothing to indicate that it happens such way. 

1) What makes Trimmomatic special about Illumina data? Accessing to adapters seems quite easy, so another tool could be used too for Illumina adapters.

2) What are your suggestions to usage of Trimmomatic? Should we always use ILLUMINACLIP parameter, or should we use it when "Overrepresented Sequences" shows the adapters in FastQC result? If it should be used, what are the default parameter values? We have seen that <adapterName>:2:30:10 is generally used, but we would like to hear your options.
Hi,

I always use  trimmomatic, since it already has the adapter sequences of differnt Illumina systems stored internally. Trimmomatic executes the parameters in the order they are stated, so I first use the `ILLUMINACLIP:TruSeq3-SE:2:30:10` parameter to remove any remaining adapters than I use the `SLIDINGWINDOW:5:20` command to remove sequence segments with a low mean quality score.

So I would always use both parameters with illumina data, since without the `ILLUMINACLIP` parameter, you would not remove any adapters.
Afterwards there should be no "Overrepresented Sequences" marked in the FastQC output as adapters.

