vg map with long assembled contigs
Entering edit mode
2.4 years ago
egoltsman • 0

Hello vgteam, Is there any progress/decision on adding the ability to map long contigs to the graph? There are several tickets that touch on this in the githup repo (, but I'm not sure what's been implemented so far.

Here is my situation. I have a set of high-quality assemblies of different individuals that I was able to build a graph with. Now I'd like to trace the paths through the graph by mapping the assemblies back to it. Going back to the original reads is not a good option here since it will likely lead to fragmented and/or false paths. I also don't care about genotyping in this case since my individuals are haploid for all practical purposes. The individuals are at least 5% divergent, and the assembly has been polished and verified. In other words, I think I could get away with a very stringent set of parameters (seed size, gap/mismatch penalties, etc). Is there anything you could recommend in this scenario?

Thank you

vg • 672 views
Entering edit mode
2.3 years ago
glenn.hickey ▴ 250

Some alternatives to vg map for long reads are - vg mpmap -S --read-length long - GraphAligner:


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