vg map with long assembled contigs
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Entering edit mode
12 months 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 (https://github.com/vgteam/vg/issues/2028), 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 • 321 views
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Entering edit mode
11 months ago
glenn.hickey ▴ 240

Some alternatives to vg map for long reads are - vg mpmap -S --read-length long - GraphAligner: https://github.com/maickrau/GraphAligner

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