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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
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Other tools to contruct GFA from genome assemblies #41

Closed ms-gx closed 3 years ago

ms-gx commented 3 years ago

Are there other tools which can generate genome graphs (GFA/rGFA format or other) de novo from genome assemblies like minigraph does? I am not talking about tools which use read alignment or VCFs for construction of graph. I want to use genome assemblies and generate the graph from them.

For a comparative study.

colindaven commented 3 years ago

@ms-gx I think vg will do this for you.

subwaystation commented 3 years ago

@ms-gx One can polish the graph from minigraph using https://github.com/ComparativeGenomicsToolkit/cactus.

A real alternative could be https://github.com/pangenome/pggb. It can generate a pangenome graph from the all versus all alignments of the de novo genome assemblies which aims to mitigate reference bias.