snpTree

snpTree constructs phylogenetic trees from concatenated single nucleotide polymorphisms (SNPs) identified in whole genome sequencing (WGS) data to support comparative genomics and outbreak investigations.

Key Features:

• Automated SNP identification: Identifies SNPs from raw reads in fastq format using BWA and from assembled contigs in fasta format using Nucmer.
• SNP concatenation: Concatenates identified SNPs based on their genomic positions relative to a reference genome.
• Phylogenetic tree construction: Constructs phylogenetic trees from concatenated SNPs using FastTree with accompanying Perl scripts.
• Data type versatility: Supports analysis of both raw sequencing reads and assembled genomes/contigs.

Scientific Applications:

• Outbreak investigation and epidemiology: Differentiates closely related outbreak isolates with minimal genetic diversity through precise SNP-based phylogenies.
• Method validation: Applied to bacterial WGS datasets including Vibrio cholerae, Staphylococcus aureus CC398, Salmonella Typhimurium, and Mycobacterium tuberculosis, showing concordant results with published analyses for the first three datasets while not replicating extensive SNP filtering reported for M. tuberculosis.

Methodology:

Align fastq reads to reference genomes with BWA and process fasta contigs with Nucmer; concatenate identified SNPs by reference-based genomic positions; construct phylogenetic trees from concatenated SNPs using FastTree with Perl scripts.