I was looking for a software that finds mutations and/or variants in bacterial genomes. Could you please give me some suggestions about which is the best one and how do they generally work ?
Before posting this question, I saw something on Google and also here in this community I found this post Identifying Non Synonymous mutations in bacterial genomes, in which they mention for example FreeBayes . I saw that this software (together to many others) is based on the alignment of reads of the query sequence with the reference sequence.
However, if I have the reference genome sequence (its complete sequence genome, the CDS file with the sequences of the genes) and the sequence of a variant (its complete sequence genome, the CDS file with the sequences of the genes and, so, I have no reads) and I want to check where mutations are , so which genes had non synonymous mutations and which others synonimous etc,... how can I do ? Or can this kind of analysis be done only with reads of the query sequence (by "query" I mean my variant genome) ?
Hoping that it is not a very silly question, I thank you in advance.