Hello

I am trying to call Intra-Species genomic variations. I do not have Raw Reads for the same. Is it a good idea to call genomic variations from assembled genomes since they are high confidence assembled nucleotides from the raw reads? (People say that small errors can be incorporated since there are no phred score, or we may miss several genomic regions since assembly software may or may not include). If we have assembled genomes which is an output of Best of the raw reads isn't it better to use assembly?

I am trying to use SNIPPY pipeline for the same. When SNIPPY call variations from assembled genomes they break the assembled genomes into small virtual raw reads (false reads). How efficient is the method compared to SNIPPY running from raw reads? What can I do if I don't have raw reads?

Reference: https://github.com/tseemann/snippy

Thank you

Kausik