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Hi
I am new to graph analysis and was sent here by Erik Garrison (https://github.com/GFA-spec/GFA-spec/issues/123)
Could someone guide me on which odgi command(s) to use to achieve my goal of ge…
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A faster way to hand off output to assemblers; can include coverage information
Spec: http://lh3.github.io/2014/07/23/first-update-on-gfa/
ABySS implementation: https://github.com/bcgsc/abyss/tree/g…
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Dear developer,
I want to convert the GAM to BAM format via VG surject command, but it failed because of the different attributes between GraphAligner and vg aligner. The differences are shown be…
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Hello again,
Thank you very much for updating and answering all the issues regarding vg.
I have a problem regarding the GAF and VCF files. I am trying to match the nodes from a specific genotype…
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I was trying to convert a [GFA-formatted graph produced by seqwish](http://hypervolu.me/~erik/tmp/MHC.fa.gfa.gz) to .vg format.
I used `zcat MHC.fa.gfa.gz | vg view -Fv - >MHC.fa.vg`
It took alm…
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Hello!
Thanks for Cuttlefish, it's been working nicely for me so far. I've been using the reduced GFA format for my own analysis, but have occasionally come across tools that demand the more accep…
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vg's path format is incompatible with the `P` namespace in GFA.
As such, I'm proposing an extension to the schema which would allow us to read and write the vg model in GFA.
https://github.com/GFA-s…
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When I use `.vg` graph in GraphAligner's mapping command `GraphAligner -g chr21.vg -f chr21.fq -t 88 -a graphaligner_aln.gam -x vg,` there is something error:
![image](https://github.com/maickrau/Gra…
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We have an unconditional chop when making a graph from GFA:
https://github.com/vgteam/vg/blob/5e1973315f33b5f0394f3ff0bfe88649785751ce/src/index_registry.cpp#L1822-L1830
And the chop size is set…
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I'd like to make an xg directly from a GFA, without going through .vg format.
This can be done with the xg executable. However, the resulting file is not packaged with the vg container system. This…