To make sure which perform more accurately, I tested two programs in two strategies. Actually the reason why I did do this test is that most of people in my firm say that for de novo assembly FLX is much more suitable than solexa without any evidence. So I decided to test two system, but there is no real data which I can use, so I just do simulation test of the two program which is representative for each system.
Both of them, velvet and newbler are used for de novo assembly. In case of velvet, by using De Bruijn graph methodology It carry out short read assembly with data from solexa, solid. On the other hand, newbler is software from Roche, FLX and it is based on overlap layout consensus methodology (for seeing about the algorithm refer http://www.ncbi.nlm.nih.gov/pubmed/20211242).
I will compare the results from both program in two strategies. All of read data in these tests are simulation data which were made from reference genome by computational simulation.
First, velvet with paired-end read of which length is 78 bp and insert size is 300. newbler with single read of which length is 300 bp.
second, in case of velvet from first test adding long insert library with same condition
