search

vgteam / vg

tools for working with genome variation graphs
https://biostars.org/tag/vg/
Other
1.07k stars 191 forks source link

vg construct will let you create a graph without reference paths, with different path names than Cactus #4239

Open adamnovak opened 3 months ago

adamnovak commented 3 months ago

@Robin-Rounthwaite points out that, if you build a graph with Cactus, it makes you specify a reference assembly name, and you come out with reference-sense paths scoped to that assembly.

If you build a graph from the same FASTA with vg construct, it just uses the FASTA IDs as path names, and the path names then do not match the ones created by Cactus.

We should support (or probably require?) using a sample/assembly name with vg construct, to stop people from making graphs with incompatible path coordinate spaces.