User: egoltsman

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egoltsman0
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Posts by egoltsman

<prev • 6 results • page 1 of 1 • next >
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Answer: A: vg deconstruct with path sizes
... That's great to know. Thanks! ...
written 5 days ago by egoltsman0
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vg deconstruct with path sizes
... Hi, I am wondering if there is a way to output snarls with path size information. Currently, if I go the route of 'vg snarls', then 'vg deconstruct', the vcf file contains only the variant sequences, and I am forced to parse those out and calculate the string size for each one, which is not too eff ...
vg written 7 days ago by egoltsman0
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Answer: A: passing a third-party GFA to vg tools
... I was able to do the conversion after adding the header line, adding paths, and making the segment ids numeric. Since minigraph doesn't trace the sample-path during graph construction, I had to trace them by mapping the assemblies back to the rGFA graph. I think without the paths present in the ...
written 11 days ago by egoltsman0
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vg map with long assembled contigs
... 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 h ...
vg written 5 weeks ago by egoltsman0 • updated 12 days ago by glenn.hickey140
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passing a third-party GFA to vg tools
... Hi, I'm wondering if it's possible to twist an rGFA formatted graph into a GFA form that vg tools can work with. Heng Li mentions in the minigraph paper that he tried doing that but couldn't get it to work. I guess my chances are slim, but in case some progress has been made since that format cam ...
vg written 7 weeks ago by egoltsman0
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importing a GFA2 scaffold graph
... Hi all, I'm exploring GATB with the idea of potentially replacing our custom assembly graph implementation with this wonderful library. As often the case, instead of creating an overlap graph from scratch (i.e. the reads), I'd like to jump in in the middle and import a set of 3rd-party unitigs and ...
gatb written 3.0 years ago by egoltsman0 • updated 2.7 years ago by Rayan Chikhi1.4k

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