Denovo assembly problem

[huma Asif]

I am a new on this platform and need to seek help with some queries
I am sequencing two bacterial genomes but the problem i am having is with its assembly for one of the genome i got scaffold N50 70234 and for other scaffold N50 is 3000.I have assembled these genome using SOAP denovo .I need to seek ur help in knowing is this N50 good for denovo assembly
what else i can do to improve scaffold N50 of these genomes
Regards

[Cofactor Genomics]

Were you expecting more similar N50s because the organisms were very similar?
Were the two projects sequenced to the same depth using the same library type and read configuration? How about the isolation, were both from a clean/clonal isolation?

In order for our team to make large strides in N50, we had to get very critical on sample purity, we integrated additional custom library types, and third we used both short read and long read platforms.

Jarret Glasscock
Cofactor Genomics

http://www.cofactorgenomics.com