search

metaGmetapop / metapop

A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations
MIT License
38 stars 10 forks source link

Can metapop increase its mapping criteria to solve strain-level community marcro-/micro-diversity? #12

Open ChaoLab opened 2 years ago

ChaoLab commented 2 years ago

It was stated that metapop is not optimized to study "strain-level genotypes". While since the calculation methods for metrics of macro-/micro-diversity are the same for both species-level and strain-level populations, is it possible to tune the settings to achieve this? For example, for species-level population mapping, a 95% ANI boundary is expected, the minimal identity of reads to reference can be set to 92% (lower with 3% percentage due to genome heterogeneity). For strain-level population mapping, a 98-99% ANI boundary is expected (or a higher setting as one may choose), the minimal identity of reads to reference can be set to 95 or 96%. This seems to be what inStrain sets (https://instrain.readthedocs.io/en/master/important_concepts.html#handling-and-reducing-mis-mapping-reads).

metaGmetapop commented 2 years ago

Hi ChaoLab - yes you can adjust the parameters to change the %ID ANI boundaries by adjusting the --id_min.