I am using four different libraries of read size 76bps, insert sizes are 300bps, 1kb, 8kb and 12kb. Expected genome size is 80MB.
I am running velvet using these four libraries. Actually I tried velvet first for different k-mers and then for the best
k-mer I tried different
cov_cutoffs. In all these assemblies from same
k-mer (69) with different
cov_cutoffs, I used the same
Sequences files from the initial
velveth run (
K-mer 69 and cov_cutoff default).
Surprisingly I got
10MB of N50 and 23MB of largest scaffold size using
cov_cutoff of 12 (median coverage is 30.76 in Log file) on the previously generated Roadmap and Sequences files. Then later I tried all new assembly from the same reads,
K-mer 69 and
cov_cutoff 12, now my
N50 is 2MB and largest scaffold size is 6.78 MB.
Later I tried the same input files and same velvet parameters and I figured out that velveth is generating different Roadmap file for the same k-mer 69, for all three runs. What could be the reason behind this? In this case it is not possible to regenerate the results.
I would really appreciate your comments on this.
Best regards, Rahul