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Can vg take MUMmer output as input?

I have a MUMmer delta file. What commands do I run to import this file into vg for genome graph construction and indexing?

vg
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updated by Ram Ram • written by ac2278 • ac2278

Always mention what you've tried and where exactly you run into a problem.

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written by Ram Ram

I think what he/she mean is whether we can use the output delta file of MUMmer (the whole-genome alignment of several de novo assemblies) like the Cactus for building the pangenome graph? I have the same question since there is hal2vg script in the cactus website while we do not know how to transfer the output of mummer to vg input. Thanks

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written by wangjing368 • wangjing368

I think what he/she mean is whether we can use the output delta file of MUMmer (the whole-genome alignment of several de novo assemblies) like the Cactus for building the pangenome graph? I have the same question since there is hal2vg script in the cactus website while we do not know how to transfer the output of mummer to vg input. Thanks

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written by wangjing368 • wangjing368

1 answer

get the sv from delta and u can set them as input of vg

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written by Qi • Qi

Care to elaborate with maybe some pseudocode and also fix your answer so it doesn't read like SMS jargon? We're on a professional forum, please write like you'd write on official communication (like a presentation or a document meant for wider consumption).

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written by Ram Ram

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