bgcflow integration with panalleleome

[anpanche]

No description provided.

[matinnuhamunada]

Hi @anpanche, thanks for the PR. I have some questions before starting the integration process. What are the differences between this two repositories?

• https://github.com/anpanche/Core-Alleleome
• https://github.com/anpanche/PAN_Alleleome

[anpanche]

Hi @anpanche, thanks for the PR. I have some questions before starting the integration process. What are the differences between this two repositories?

• https://github.com/anpanche/Core-Alleleome

• https://github.com/anpanche/PAN_Alleleome

The core alleleome finds the sequence diversity of only core genes of the pangenome. The core genes represent the set of genes which are present in >90% strains.
The qcqa process in alleleome analysis checks for the presence of genes in atleast 5% of strains and further removes those genes that don't satisfy the condition.
Since core genes represent the set of genes present in >90% strains, this step is not necessary for it.
In pangenes(core, accessory and rare)this step is essential and it will affect the gene sets to be carried forward for the alleleome.In PAN alleleome this step is introduced.

[matinnuhamunada]

Hi @anpanche, thanks for the PR. I have some questions before starting the integration process. What are the differences between this two repositories?

• https://github.com/anpanche/Core-Alleleome
• https://github.com/anpanche/PAN_Alleleome

The core alleleome finds the sequence diversity of only core genes of the pangenome. The core genes represent the set of genes which are present in >90% strains. The qcqa process in alleleome analysis checks for the presence of genes in atleast 5% of strains and further removes those genes that don't satisfy the condition. Since core genes represent the set of genes present in >90% strains, this step is not necessary for it. In pangenes(core, accessory and rare)this step is essential and it will affect the gene sets to be carried forward for the alleleome.In PAN alleleome this step is introduced.

Can't this two repository be merged together and then you introduce the CLI to whether run the Core or Pan pipeline?

[anpanche]

Yes, this can also be done.

[anpanche]

Hi @matinnuhamunada ,
which kind of integration will be more convenient? So I can work accordingly. If we decide to integrate corealleleome with panalleleome how it would be used in bgcflow? What changes I need to make and additional scripts to be written?