Ilia Minkin
Ilia Minkin
Yes, the whole point of the compacted graph is to compress identical substrings of length at least k into integers. Those integers are much easier to index and compare: if...
Hi, Thank you for the suggestion! I will consider adding an API interface in the future version(s).
Hi Erik, Thanks for reaching out. > I thought it was TWO PAss COnstruction (becauses it uses a two pass, or multi-pass, construction algorithm). Almost! It is TWO PAss COmpaction...
Hi @rob-p, I will take a closer look, but for now: what is wrong with having the same k-mer at the start and end of the segment? There could be...
Hi @rob-p, Sorry for a late reply. The issue here is that we assume different models for handling double strandness of the DNA. You assume that: > However, since we...
> However, my understanding now is that, instead, k-mers are canonicalized, so that if the reverse complement of a k-mer appears somewhere else on the reference in the same orientation,...
Note that though "ACTG" and "CAGT" are reverse complement of each other, they yield different nodes and edges. But becuse "ACTG" is also present on the reverse strand, it will...
Hi @rob-p, Sorry for a late reply. I think you are right.
Hi, @coryVkeith I do try my best to maintain the code. I will try to reproduce the error and get back to you.
Hi, I am glad that you found SibeliaZ helpful. This is a bit tricky question. Representation of whole-genome alignment is inherently ambiguous. For example, a single alignment block can be...