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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
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The main difference between minigraph and PGGB pipeline #54

Closed biozzq closed 2 years ago

biozzq commented 2 years ago

Hi,

Recently, i want to map the short-sequencing reads to the graph genome using recently published giraffe. The first thing I need do is to generate a high-quality and no-reference bias graph genome. I found that the vgteam recommend us to use PGGB pipeline (https://github.com/pangenome/pggb) to generate the graph genome as data model mismatch between minigraph and vg (https://github.com/vgteam/vg/issues/3492#issuecomment-985250761). Could you give more comments about the differences between minigraph and PGGB pipeline? Thank you in advance.

Sincerely, Zheng zhuqing

lh3 commented 2 years ago

Sorry for the late response. pggb is more powerful as it records base differences and per-haplotype paths. Minigraph on the other hand is faster and is more convenient if your focus is SVs. If you have bandwidth, I would recommend to try both and see what fits your project better.