Hi, @lh3
Protein is conserved across the tree of life, but it may not have enough synteny in the complex repeat region or complex genome. Could be possible to use any pre-aligned markers (eg. panTE annotation from RepeatMasker, centromere annotation from SRF)? It may be out of the scope of pangene, but if it takes PAF and marker to build a graph, maybe we can also feed other pre-aligned markers.
Hi, @lh3 Protein is conserved across the tree of life, but it may not have enough synteny in the complex repeat region or complex genome. Could be possible to use any pre-aligned markers (eg. panTE annotation from RepeatMasker, centromere annotation from SRF)? It may be out of the scope of
pangene, but if it takes PAF and marker to build a graph, maybe we can also feed other pre-aligned markers.