snippy

Snippy executes rapid, parallelized haploid variant calling and core genome alignment for Next-Generation Sequencing (NGS) reads.

Snippy is the go-to bioinformatics tool for high-speed variant analysis: it precisely identifies Single Nucleotide Polymorphisms (SNPs) and insertions/deletions (indels) by aligning NGS sequence reads against a haploid reference genome. Developed by Torsten Seemann, Snippy is designed for efficiency, leveraging multi-core CPUs to quickly generate a consistent output folder containing VCF, BAM, and consensus FASTA files. Crucially, it integrates with `snippy-core` to produce a core SNP alignment, a foundational step for building robust phylogenomic trees from multiple isolates (e.g., in bacterial outbreak analysis).

https://github.com/tseemann/snippy