Is it possible to merge/combine three genome into one?

Question

[Kumar]

I have three bacterial draft genomes (sequenced by illumina and ABI solid sequencing platform), belongs to same species (Average Nucleotide Identify value is 99.9% for each other). I would like to merge/combine those three genomes into singe genome, so that I could gain the missing regions of each other genome. Thus would help me to represent the combined single genome for my Pan-genome analysis. Please let me know, is it possible to do, if it so please help me.

Thank you in advance.

[ashish]

do you want to create a pan-genome using these three draft genomes?

[Kumar]

No Ashish, I have 30 bacterial genomes including above mentioned three genomes. But, as per pan genome analysis If i include those three genome, I may end up with less unique gene numbers, because of accessory genes sharing among those three genomes. That is why, I would like to combine those three genomes into one. So that I will be having 28 genomes for my pan genome analysis. Thus would help me to find more unique gene.

Answer 1

[Bastien Hervé]

If I got you right you are trying to get unique parts of your 3 genomes to create a single one without redundancy. I do not think you can do that in a linear standard way.

If you want to analyze your genes of your 28 genomes based on your 3 other genomes you can try Prokka

If you want to align or process variant detection you can try this tool (never tested)

[Kumar]

Thank you Bastien. As you said, I would like to reduce the redundancy of those three genomes. At the same time I should choose only one genome among the three. By choosing one genome, I should not miss any regions/gene of the omitted genome aswell. That is why I though to merge those three genome into single one. However I would try the vg tool as you suggested.

I have annotated all the genome by Prokka only. I do not understand, how does prokka help in this regard?

[Bastien Hervé]

Prokka would have help if you were looking at gene location on your genomes

Answer 2

[WouterDeCoster]

I think you could just use a long read assembler here, such as miniasm.

[Kumar]

Thank you, I would try miniasm pipeline as you suggested.