There are few of assembly tools can handle the question of hybrid assembly of NGS data, it is also my puzzle, because the sequence type and error type are different, here is a great review to introduce the difference: Michael L. Metzker, Sequencing technologies — the next generation. Nat Rev Genet. 2010 Jan;11(1):31-46. Epub 2009 Dec 8. Review.
Maybe some software do it well, although they are not suitable for me:
MIRA - Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina
ABySS - Assembly By Short Sequences - A de novo sequence assembler, "ABySS is a de novo sequence assembler that is designed for very short reads.
ALLPATHS - a whole genome shotgun assembler that can generate high quality genome assemblies using short reads such as those produced by the new generation of sequencers.
ALLPATHS-LG - a update version of ALLPATHS. It works on both small and large (mammalian size) genomes.
Or you can assemble them using Newbler for 454 reads and Velvet for Illumina reads as you did, then use PHRAP(Phrap is a program for assembling shotgun DNA sequence data, suitable for sanger and 454 reads, it used overlap-layout-consensus algorithm), CPA3/PCAP (CAP3 is for small-scale assembly of EST sequences with or without quality values;PCAP is for large-scale assembly of genomic sequences with quality values and with or without forward-reverse read pairs) and Euler(Euler is a new approach to fragment assembly that abandons the classical "overlap - layout - consensus" paradigm that is used in all currently available assembly tools.) to combine the contigs, if you wan to construct scaffolds, you can try SSPACE(Tools for scaffolding pre-assembled contigs), PE-Assembler(PE-Assembler: de novo assembler using short paired-end reads) etc.
For this question, I also have an article recommend to you:
Miller JR, Koren S, Sutton G. Assembly algorithms for next-generation sequencing data. Genomics. 2010 Jun;95(6):315-27. Epub 2010 Mar 6.