SNP Analysis

 

SNP = Single Nucleotide Polymorphism SNP analysis = identifying and interpreting single‑base differences between genomes.

What it answers

• How different are two strains?

• Which mutations define a lineage?

• Are mutations under selection?

• What is the evolutionary distance?

Two ways to do SNP analysis

A. Using FASTQ (raw reads) → TRUE variant calling

Pipeline:

1. Align reads (Bowtie2, BWA)

2. Call variants (bcftools, FreeBayes, GATK)

3. Produce VCF

4. Filter + interpret

This is the gold standard.

B. Using FASTA assemblies → whole‑genome alignment

Tools: MAFFT, Parsnp, snippy-core This is not true variant calling, but you can still extract SNPs.

 

Think of it like

Comparing two books line‑by‑line to find spelling differences

 

How these tools fit together in real workflows

If you have FASTQ reads

• Bowtie2 → align

• bcftools → call SNPs

• MACSE → align coding regions

• HyPhy → selection analysis

If you have Nanopore reads

• Epi2ME → basecalling + variant calling

• Or run your own pipeline

If you have FASTA assemblies

• Use for AMRFinderPlus

• Use for pangenomes (Panaroo)

• Use for whole‑genome SNP alignment (not variant calling)

 

 

 

 

 

 

 

 

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