I am having trouble finding a program that will preform a de novo assembly on unassigned reads from an illumina fastq. Are there any good programs that preform this function or have a output of unassigned reads that can be pipelined
You can begin with Velvet or SOAPdenovo2 that perform de novo assembly on Illumina read sequences.
I would try to assemble all reads (assigned together with not assigned one) so you should obtain contigs from both origin. Similarity search on the resulting contigs could be helpful to identify this origin.