search

phiweger / zoo

A portable datastructure for rapid prototyping in (viral) bioinformatics (under development).
5 stars 2 forks source link

support variant graphs #128

Open phiweger opened 7 years ago

phiweger commented 7 years ago

https://github.com/vgteam/vg

phiweger commented 7 years ago

represent graph in JSON:

phiweger commented 7 years ago

note: some collections of viruses are so diverse, that there is no real gain in storing them in a variant graph. so both - a flat sequence as well as a variant/ assembly graph' should be supported, where a linear sequence can be seen as a graph with one node and no edges.

also, a valiant graph has a 1 : n mapping (one graph, n documents) while has assembly is a 1 : 1 mapping.

phiweger commented 7 years ago

basically assume the sequence field to be a graph and offer corresponding functionalities (annotations need to hold the corresponding coordinates).