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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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How to get the index (.xg) of .vg file ? #1028

Closed ggoodstudydaydayup closed 1 year ago

ggoodstudydaydayup commented 1 year ago

Hi, I am trying to use minigraph-cactus. And I'm not sure how to get the .xg file. The pipeline of D. Melanogaster Pangenome Methods can be seen below. "cactus ./js 16-fly-pg-2022-05-26-seqfile.txt ./softmask.fly.hal --realTimeLogging --logFile softmask.fly.hal.log" "hal2vg ./softmask.fly.hal --noAncesstors > fly-cactus.vg" After these steps, shall I use this command "vg index -x fly-cactus.xg -k 16 fly-cactus.vg" to construct the index of .vg file? Best wishes, Yu Liu

glennhickey commented 1 year ago

I'd recommend using cactus-pangenome to make your graph. It will output a .gbz file (with --gbz and/or --giraffe options) that you can use will most vg tools (in place of an .xg).

But yeah, you can indeed convert .vg to .xg with vg index -x (or vg convert -x). But I warn you that the output of progressive cactus converted this way will be difficult to use with vg.

ggoodstudydaydayup commented 1 year ago

Thanks for your reply !