My purpopse is to get the unique region among multiple genomes of different strains of same species. their genome size will be 600 MB- 5 Gb. I came across few of the softwares nucdiff, Mauve, CHROMEISTER, Lastz. Among them nucdiff seems to solve my problem since it gives all variants including SNPs, structural variants etc., but the problem with nucdiff is that it cannot compare multiple genomes at one go. Any suggestions will be highly appreciated.
Thanks in advance.
This approach is computational intensive and not logical. You probably won't find any tool doing that.
Abhijeet Singh whether any other approach like using OrthoFinder will work. which can give genome specific genes..??
This approach is surely better than direct MSA with whole genome sequences. But, still if genomes are similar, the orthogroups will be huge which will be significantly costly = time as it also performs MSA & tree building. Further, orhtogroups = similar genes/sequences and you wanted to find unique regions, thus this tool will not provide you any direct results and you have to dig in the data to get what you want.
Your suggestion is good but I won't completely agree to what you just said. Orthofinder does not give genome specific genes... it will give you similar genes/orthologs shared by all genomes. There is a huge difference in your statement and orthologs.
Abhijeet Singh by running OrthoFinder we get the Orthogroups_UnassignedGenes.tsv which gives the list of genes unassigned to any orthogroups for the species compared. These genes from one species can be blastp searched to the orthologs of other species and vice-versa to get gene specific gene something like that I found here https://www.biostars.org/p/384067/ . reference paper attached.
Please suggest.
As I mentioned earlier, you have to work around the data to get what you want. You will not get direct answer from Orthofinder analysis.
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