Thank you, but still I am confused. Actually, I am working with the tool , BBsplit. I want to split the reads I have according to the reference genome to which it maps. So, after i run bbsplit, if we used paired end reads, the tool gives an output in such a way that, the paired end reads that map to a particular reference genome is put together and the ones which did not map are given as seperate output. For example :

command :bbsplit.sh in1=reads1.fq in2=reads2.fq ref=ecoli.fa,salmonella.fa basename=out_%.fq outu1=clean1.fq outu2=clean2.fq output : out_ecoli.fq, out_salmonelaa.fq, clean1.fq and clean2.fq. , where the out_ecoli and out_salmonella are paired end reads that mapped to reference genome of ecoli and salmonella and clean1 and clean2 are forward and reverse reads which did not map to any reference genome. And bbsplit manual says that BBSplit is a tool that bins reads by mapping to multiple references simultaneously, using BBMap. The reads go to the bin of the reference they map to best. There are also disambiguation options, such that reads that map to multiple references can be binned with all of them, none of them, one of them, or put in a special "ambiguous" file for each of them. Paired reads will always be kept together.

So the out_ecoli or out_salmonella, are they paired end reads which are interlaced or are they joined because they overlap?