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vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
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How to build a pangenome graph for some de novo genomes? #3125

Open Xuelei-Dai opened 3 years ago

Xuelei-Dai commented 3 years ago

Hello, I want to know if I have some de novo genomes to build a graphical pangenome, except the recommended method https://github.com/pangenome/pggb, whether the minigraph https://github.com/lh3/minigraph is a good way to get the gfa file?

Best wishes

ekg commented 3 years ago

Both ways will work. You can try them and compare. pggb will give you a full graph with all input sequences and also a consensus graph representing unique sequences in the pangenome. Minigraph will also give a consensus graph which it builds up progressively.

On Mon, Dec 14, 2020, 11:04 fantasticair notifications@github.com wrote:

Hello, I want to know if I have some de novo genomes to build a graphical pangenome, except the recommended method https://github.com/pangenome/pggb http://url, whether the minigraph https://github.com/lh3/minigraph http://url is a good way to get the gfa file?

Best wishes

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