Ilia Minkin

Hi @blaiseli, thank you for checking this thoroughly. It seems that there is some issue with the MAF file. I will take a closer look at the file and the...

Hi @rob-p , I understand you confusion. The issue is that initially we adopted the edge-centric definition of the graph, i.e. sequences are spelled by edges, with nodes of size...

@rob-p I was afraid the odd/even issue was going to pop-up. I will think about it and try to make a fix soon.

Hi, It seems that the compiler cannot find the library for some reason. From my point of view, the easiest way to install TwoPaCo is using bioconda (https://bioconda.github.io/). Alternatively, you...

Thanks for reporting this. I pushed a quick fix to the 0.9.4 branch. However, I can't test it on my machine since the error seems to be caused by a...

Sorry for a late reply, to do the whole thing from scratch try the following: mkdir TwoPaCo-0.9.4 git clone https://github.com/medvedevgroup/TwoPaCo git checkout 0.9.4 mkdir build cd build cmake .. make

Hey @rickbeeloo , did it finish? Do you have enough free space on the disk?

How much memory does your machine have and what was the command line you used to run twopaco? I would suggest using the largest filter size possible given your machine's...

Indeed, for each node in the graph, we can either choose either its positive or negative strand as the "reference" representation in the GFA file. In the example you provided,...

Honestly, I think the best format suited for your purpose is [the junction list format](https://github.com/medvedevgroup/TwoPaCo#junctions-list-format). SibeliaZ basically works using some form of it, and it is the simplest possible (at...