I'm trying to check the synteny of my genome assembly with the reference genome (same species) to see if there's sequence missing due to gaps in my assembled genome. Any recommendations on which software to use?
for prokaryotic genomes: SIbelia or Mauve
Alright thanks for the info!
You can try mySyntenyportal.
This review from 2020 summarizes 16 different tools for synteny detection on their Table 2:
One can easily look into each program's paper for more details using citations on the table as well.
note that doing a whole-genome-alignment based synteny analysis may have different strategies to gene (or "marker") based synteny analysis (many of the strategies in that link use the marker based synteny analysis, e.g. aligns the proteins from gene predictions in each genome. see the input data in the table 2). also, depending on the size of your genome (eukaryotic or prokaryote) may affect your choice of synteny tool. similarly, since you are looking at same species, the alignment parameters may be a little different also. aligning genome to genome with minimap2 might be sufficient.
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