Mikko Rautiainen
Mikko Rautiainen
The graph and the read would be very helpful if you could upload them somewhere
Hi, the output GAF has the mapping quality column which can be used to compare alignments which span the same area. You can filter by mapping quality for example with...
You can filter by identity to remove spurious alignments but I would suggest against using it to pick the best match among the secondary alignments. The issue is that the...
You can use multiple output formats at the same time in GraphAligner, for example `-a alignments.gaf -a alignments.json` will write both. If you filter the alignments afterwards then you would...
The reason for the lower limit is because random alignments have an about 50% identity so a lower cutoff will treat random alignments as valid alignments. Can you say a...
Hi, could you share the graph and the read?
It was removed to simplify the code. I didn't know anyone used `--global-alignment`. For now you can use eg. commit 5217838 which has both `--global-alignment` and `--multiseed-DP`
This functionality is no longer supported as of v1.0.15 and later. The reason is that sometimes assemblers might output * edge overlaps when there is an overlap. GraphAligner now requires...
There's currently no plan to add an option for that. Do the other tools you use require * overlaps? If not, my suggestion would be to replace the overlaps with...
The parameters are hidden because it's meant for a very specific use case. You can use them with the same parameters we will use in an upcoming version of verkko:...