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lh3 / pangene

Constructing a pangenome gene graph
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Aligner effect for local graph inference #4

Closed baozg closed 10 months ago

baozg commented 1 year ago

Hi, @lh3

Does the aligner have effects on pangene inference? Or pangene has some inside control. I am trying to infer the duplication number of non-ref individuals with A.thaliana HiFi assemblies. I use miniprot, lifoff and minimap2 -x splice for mapping cds or protein sequences. Here are the dot plots. Since the overall synteny is quite good in A.thaliana, miniport looks like it has more false hints. How does this affect the final graph? Could we also use minimap2 -x splice for cds mapping to build graph?

miniport --outc=0.9 --outs=0.9 --no-cs -Iu
minimap2 -x splice 
liftoff -p {threads} -sc 0.9 -copies -g {input.gff} -u {output.umap} -o {params.gff} -dir {params.tmpdir} -cds -polish
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baozg commented 1 year ago

Filtering by identity in miniprot tags, could past whole genome duplication influence it in the past?

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