Suggestions for better and accurate tool for PanGenome analysis.

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6.3 years ago

Dattatray Mongad ▴ 380

I am doing pan genome analysis of multiple genera. I am searching a tool which will work on protein files (I have annotated proteins for each genome). I wanted to run Roary, but it requires .gff files as well.

Any suggestions are welcomed.

sequencing genome gene pangenome • 1.8k views

ADD COMMENT • link 6.3 years ago by Dattatray Mongad ▴ 380

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Something like CD-HIT and then parse the output? probably it would works as first insigth to what you want to do, however I think this is a complicated job even for closely-related species, so, for multiple genera... please tell me if you find another suitable solution.

ADD REPLY • link 6.3 years ago by Buffo ★ 2.4k

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OrthoMCL/PorthoMCL/JustOrthologs.

(Fair warning, OrthoMCL is an absolute pain in the ass to use)

What organism is it?

ADD REPLY • link 6.3 years ago by Joe 21k

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I have several microbial genomes and protein files from multiple genera. I have tried BPGA but it cantbe automated.

ADD REPLY • link 6.3 years ago by Dattatray Mongad ▴ 380

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Roary is the best tool to use. It will accept gbk inputs (or at least it certainly used to)

You could reannotate with prokka to get a gff if you really needed to.

ADD REPLY • link 6.3 years ago by Joe 21k

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