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Pangenome: Gene presence and absence analysis

Hello. I would like to have an idea for gene presence and absence determination for pangenome analysis.

I have built a pangenome from several yeast strains of interest by merging each CDS and eliminate the redundantly using CD-HIT. Then, I mapped Illumina reads from each strain against the pangenome individually, generated sorted-bam files and calculated mean coverages by qualimap. Based on this information (e.g., mean coverage), I want to determine each CDS cover ratio and define the CDS presence if 95% of it is covered by reads. Do you have any idea how to run this step or a better idea? By looking over previous discussions, I have tried to use samtools depth and got read depth per each single base location. However, I still wondering how to transform the data, calculate each CDS cover ratio, and use for pangenome analysis. Thank you for your support.

sequencing pangenome
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updated by colindaven colindaven • written by ysas • ysas

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Very late (only 3.5 years), but I have used odgi pav successfully for this. There is a nice tutorial here:

https://odgi.readthedocs.io/en/latest/rst/tutorials/presence_absence_variants.html

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written by colindaven colindaven

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