Assigning Clades from SNPs

General
1

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

2

In the documentation, specification on clades is done with AA-changes - is this also possible with nucleotides?

Yes this can be done in augur clades - there’s some docs here and we use nuc mutations to define our SARS-CoV-2 clades.

There are also SNP typing PCRs for these SNPs - is it possible to automatically link this PCR-primers?

Augur doesn’t consider these, but Nextclade has the ability to identifying mutations in (specified) primer sites. There may be better tools to answer your exact question however.

Best,
james

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