I want to assign clades (and subclades) to my bacterial sequence data. All of these motifs are SNP on the chromosome. In the documentation, specification on clades is done with AA-changes - is this also possible with nucleotides?
My clades are pretty static (since it is a monophyletic organism B. anthracis).
Can I define clades by SNP status when I give these SNPs ? (like in the CanSNPer algorithm)
Input files would look like this:
#SNP Organism Reference Strain Position Derived_base Ancestral_base
A.Br.001 Bacillus_anthracis VanErt2007 Ames 182106 C T
A.Br.002 Bacillus_anthracis VanErt2007 Ames 947759 T G
A.Br.003 Bacillus_anthracis VanErt2007 Ames 1493157 C T
A.Br.004 Bacillus_anthracis VanErt2007 Ames 3600659 C T
A.Br.006 Bacillus_anthracis VanErt2007 Ames 162509 A C
A.Br.007 Bacillus_anthracis VanErt2007 Ames 266439 G A
A.Br.008 Bacillus_anthracis VanErt2007 Ames 3947248 C A
A.Br.009 Bacillus_anthracis VanErt2007 Ames 2589823 G A
B.Br.001 Bacillus_anthracis VanErt2007 Ames 1455279 G A
B.Br.002 Bacillus_anthracis VanErt2007 Ames 1056740 A C
B.Br.003 Bacillus_anthracis VanErt2007 Ames 1494269 A G
B.Br.004 Bacillus_anthracis VanErt2007 Ames 69952 C T
A/B.Br.001 Bacillus_anthracis VanErt2007 Ames 3697886 A G
There are also SNP typing PCRs for these SNPs - is it possible to automatically link this PCR-primers?
So e.q.: Found an isolate in Bavaria, Germany, other isolates in Bavaria are B.Br.003 so that it automatically recommends these SNP-PCRs (before sequencing) as what I filtered?
Best regards