I am new to SNP. I am looking for some help. My PI suggested me to call snps with de novo assembly . I have 100 bacteria draft assembly (each assembly has multiplex contigs). Should I use mummer (nucmer) to align each draft genome to the reference, call the SNP. After that combine all the snps into one file? I checked the mummer, It seems mummer could not align multiple draft assembly to one reference. If I am right, what tool I could use to combine the SNPs from different assembly in to one file? Thank you very much!