TakeABreak can use paired-end and mate pair reads as well as single-end ones, it just does not use the pairing or mating information. You can indicate in the input that some fastq files come from the same sample, using files of files (fof). For instance, if you have three samples, each represented by two files (one for each mate), you can run TakeABreak as follows:
./TakeABreak -in path/DATA/data_3indiv.fof
The file data_3indiv.fof contains 3 lines such as :
indivA.fof indivB.fof indivC.fof
With indivA.fof file, being located in the path/DATA directory and containing the following two lines :
This is documented in TakeABreak Readme : https://github.com/GATB/TakeABreak and this is a feature of the GATB-core library, so you can do this for a majority of tools developped on top of GATB.
I hope this answers your question.