Closed Franny97 closed 3 years ago
Hi,
It is explained in the wiki:
https://github.com/ndierckx/NOVOPlasty/wiki/Interpretation-&-post-processing
It is impossible to resolve the orientation of the region between the inverted repeat so it creates an additional contig.
Different output files are explained here: https://github.com/ndierckx/NOVOPlasty/wiki/Output-files
If you use a reference genome, it will resolve the contigs automatically and you will get one circular contig
Hi,
Thanks for your reply. The problem is that the k-mer distribution is like this for each contig generated. Then is it still normal to obtain certain k-mers that are repeated twice in the assembly only because of the inverted repeats?
Thanks for your quick reply.
of course, the inverted repeat is completely identical, many kmers will map to both Each contig has an inverted repeat, so that is normal
I don't really understand what the problem is, all cp genomes have inverted repeats?
No, all the assemblies generated with the test files provided, (so one for each inverted repeat possibility) have this k-mer distribution. Initially i thought it was a problem but it is normal to see this if we consider the inverted repeats.
Thanks for your help.
Hello,
We have tried doing the assembly using the test set for chloroplasts that you provide on this GitHub repository and we analyzed the assembly. We generate 3 different contigs, which form 2 distinct assemblies.
When analyzing the k-mer distribution with kat, this is what we obtain:![contig2Reads1-main mx spectra-cn](https://user-images.githubusercontent.com/77974088/105713598-a1e7a280-5f1b-11eb-8c19-7c57c65f4a18.png)
Do you have any idea why the assembly is redundant?
Thanks a lot