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Questions about diploid assembly vs. haploid reference genome analysis #290
Description
Hi，
I am doing the assembly and analysis of a diploid species whose reference genome is haploid. My assembly didn't distinguish between haploids, so the Syri analysis suggested that it contained a lot of inverses and didn't produce valid results. Does this mean that haploid versus diploid variant analysis cannot be performed directly? Do I need to assemble a haploid before I can analyze it with a reference genome?
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lrauschning commentedon Jun 23, 2025
Hi Tiffany,
I'm not quite sure what you mean by "haploid vs diploid analysis". SyRI works on single linear genome assemblies. Our typical workflow is to store the two resolved haplotypes if available in separate FASTA files and name the sequences something like SAMPLE_hap1, SAMPLE_hap2 etc.