Mikko Rautiainen
Mikko Rautiainen
It will only use L lines to connect segments. The read might in addition be partially aligned across the gap with multiple alignments, so there would be two GAF lines,...
Hi, the commands for vg and GraphAligner look perfectly fine. The same issue has happened before in some machines. It seems to be related to the perfect hashing used in...
Has this occurred only when using docker or also without docker?
This is a limitation of the DP backtrace used in GraphAligner. It will only produce one alignment per backtrace which is forced to be the best alignment path, so alternative...
That option caches the seed index but only if MUM/MEM seeding index is chosen. The default parameters use a minimizer seeding index, and there is currently no way to cache...
There's no concrete plan for fixing this in the near future. It's definitely something I'd like to have fixed, but so far I haven't come across any solution that would...
Hi, could you try compiling the most recent commit and trying with that, and if it still gives errors then share the graph and the reads
Could you try with the most recent commit [7877294](https://github.com/maickrau/GraphAligner/commit/7877294fc7d6ecc78c8d92c3a408e915a0cb738c)? There was a similar bug in some other datasets, it might have fixed this one as well. About the comparison, for...
You can merge the individual chromosome graphs into one graph which has all chromosomes and then align the reads to that graph. GraphAligner will then align to all chromosomes and...
Could you share the graph?