Hi everyone, hope you all are having a good day.
So, i am trying to finish a bacterial de novo genome assembly, i have single reads, paired-end reads, mate-pair reads and an optical map, with all these data one would think the genome should have been ready for yesterday, but it isn't, i am having a really hard time with these one. I used SPAdes for the initial assembly, finished with 120ish contigs, used another tools and created some scaffolds, reached 81% of the total genome coverage (information obtained with the optical map) and at the moment i am trying to fill the gaps. I am using CLC for these(i would appreciate very much if you have any another tool of your preference in mind) and it helped a little, but still not been able of finishing the assembly. There are even some places in the genome that have no contigs or scaffolds mapping them, i try using any other close bacteria as reference but still no success.
Can you give me some more ideas? Brainstorm?
This genome is incredibly repetitive.
Anyone has already handle this kind of data?
Thanks in advance.
How deeply has the genome been sequenced? It might just be that the data is not there to piece together the genome fully without additional sequencing.
All the assemblies gave a x300 fold coverage aprox.