Visualization and SV detection after graph genome construction

lh3 / minigraph

Sequence-to-graph mapper and graph generator

https://lh3.github.io/minigraph

MIT License

411 stars 39 forks source link

Visualization and SV detection after graph genome construction #23

Closed jialei0701 closed 3 years ago

jialei0701 commented 3 years ago

Dear Prof. Li, After the construction of graph genome with minigraph, have you developed software to visualize the graph genome? And whether it is possible to carry out subsequent analysis such as SV detection based on rGAF? Thank you.

lh3 commented 3 years ago

I usually use bandage for visualization. You can use

gfatools bubble in.gfa > out.bed

to get the structural variations encoded in the graph.

jialei0701 commented 3 years ago

OK, thank you.

biozhangzhou commented 3 years ago

I usually use bandage for visualization. You can use
gfatools bubble in.gfa > out.bed
to get the structural variations encoded in the graph.

Hello,Prof. Li. what is the meaning of every column in the bubble out file ? How do you get all the SVs in you Minigraph paper and annotate it ?

lh3 commented 3 years ago

Columns are described here: ftp://ftp.dfci.harvard.edu/pub/hli/minigraph/HPP/

mgutils.js anno does annotation but it is not for endusers. You are recommended to implement your own annotation pipelines.

biozhangzhou commented 3 years ago

Thank you.