Hello There, I was trying out strainphlan and had a small doubt, below is my command:-
strainphlan -s /data/HC_Analysis_LVPEI/LVPEI/170_Healthy_Control/Strainphlan/Sam_files/consensus_marker/E1-10.pkl \
-m /data/HC_Analysis_LVPEI/LVPEI/170_Healthy_Control/Strainphlan/Sam_files/clade_markers/s__Prevotella_copri.fna \
-r /data/HC_Analysis_LVPEI/LVPEI/170_Healthy_Control/Strainphlan/Sam_files/clade_markers/GCF_020735445.1_ASM2073544v1_genomic.fna.gz \
-o /data/HC_Analysis_LVPEI/LVPEI/170_Healthy_Control/Strainphlan/Sam_files/StrainPhlan_outputs \
-c s__Prevotella_copri \
--phylophlan_mode fast \
--nproc 8
For the -r option, I am using the NCBI reference genome GCF_020735445.1 (Segatella copri DSM 18205).Is it appropriate to use this NCBI reference genome with StrainPhlAn, or should the reference genome correspond to one of the genomes used in the MetaPhlAn database (e.g., the genomes from which the s__Prevotella_copri markers were derived)?
If StrainPhlAn expects MetaPhlAn-compatible reference genomes, what is the recommended way to identify and obtain the correct reference genome for a given species?
Thank you for your help.