I have a set of paired end reads from an unknown species. I want to assemble them to find the main genome. I have a program based on the basic de bruijn graph algorithm which is for single reads. Are there any other classic algorithm which works better in the case of paired end reads.? (Or any other version of de bruijn graph algorithm) Also I have 3 versions of these reads from 3 sample of the same species. Could them help me to improve my assembler?
There are heaps of De Bruijin graph implementations for paired end reads:
DISCOVAR (needs 250 bp paired reads, PCR-free) https://software.broadinstitute.org/software/discovar/blog/?page_id=23
ALLPATHS-LG (needs matepaired data) http://software.broadinstitute.org/allpaths-lg/blog/
and many many many more
As for your three versions from three samples, do you expect the samples to be different? If they're replicates (identical) then you can treat them as three libraries in the assembler and assemble it all together.