core genome evaluation

Core genome evaluation

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Core genome evaluation isn't an independent tool, but a custom python script created for this workflow.

To help the users interpret the quality of their core genome analysis, the core, shell, and cloud genes are counted and put into an easy-to-digest csv file. This file can be used to eliminate samples that do not match the others. Ideally, 90% of the genes of an isolate would be included in the core genome, but different environments and circumstances may require a reduction in that threshold.

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Example file for a run (core_genome_evaluation.csv)

sample,total,core,soft,shell,cloud,per_core,per_soft,per_shell,per_clouc,length,num_ambiguous,per_ambiguous
GCF_000834105.1_ASM83410v1_genomic,778.0,292.0,0.0,486.0,0.0,0.37532133676092544,0.0,0.6246786632390745,0.0,279676.0,3046.0,0.010891174072855734
GCF_000972335.1_ASM97233v1_genomic,993.0,292.0,0.0,701.0,0.0,0.2940584088620342,0.0,0.7059415911379657,0.0,279676.0,6991.0,0.02499678199058911
GCF_000788095.1_ASM78809v1_genomic,3888.0,292.0,0.0,3596.0,0.0,0.07510288065843622,0.0,0.9248971193415638,0.0,279676.0,4042.0,0.01445243782090705
GCF_000978875.1_ASM97887v1_genomic,4000.0,292.0,0.0,3708.0,0.0,0.073,0.0,0.927,0.0,279676.0,5716.0,0.020437935325161975
GCF_000758465.1_ASM75846v1_genomic,4000.0,292.0,0.0,3708.0,0.0,0.073,0.0,0.927,0.0,279676.0,3382.0,0.012092564252921238
GCF_000742995.1_ASM74299v1_genomic,4546.0,292.0,0.0,4254.0,0.0,0.06423229212494501,0.0,0.935767707875055,0.0,279676.0,2986.0,0.01067664011212975