Snippy-NG
Synopsis
🚨 This software is still under development 🚨
snippy-ng is a modern version of the classic snippy tool.
It finds variants in haploid microbial
genomes relative to a reference genome.
It can accept short reads, long reads, or
assembled genomes.
It can also combine the variants from multiple
samples to make a multiple sequence alignment
and a phylogenomic tree.
Final results can be viewed from an interactive
HTML report.
Documentation
Installation
Install script
curl -sSL https://cpg.org.au/snippy-ng/install.sh | bash -s -- --force
Conda
Will be available on first official release.
Quick Start
snippy-ng short --ref tests/data/reference.gbk --R1 tests/data/mutant_R1.fastq.gz --R2 tests/data/mutant_R2.fastq.gz
snippy-ng asm --ref tests/data/reference.gbk tests/data/wildtype.contigs.fa
export CLAIR3_MODELS=./clair3_models # try to find appropriate models in this directory
snippy-ng long --ref tests/data/JKD6159.fasta tests/data/JKD6159.fastq.gz
snippy-ng utils gather --json --ref tests/data/reference.gbk tests/data/{wildtype,mutant}* > samples.json
snippy-ng multi samples.json --cpus 6 -o multi
snippy-ng tree --fast multi/core/core.095.aln -o multi/tree
snippy-ng utils report tree multi/tree/tree.snps.newick --metadata multi/snippy.vcf.summary.tsv -o multi/report
Development
To set up a development environment, clone the repository and install pixi and hatch. Pixi is used to manage external dependencies, and Hatch is used to manage the Python package development.
git clone git@github.com:centre-pathogen-genomics/snippy-ng.git && cd snippy-ng
# install pixi if not already installed
curl -fsSL https://pixi.sh/install.sh | bash
# install hatch if not already installed
pixi global install hatch
Activate the pixi environment and launch a hatch shell. This will install all dependencies and set up the development environment.
pixi shell
hatch shell
snippy-ng --help
Testing
Run the default fast test suite with:
pixi run test
Run the simulation-backed integration tests with:
pixi run -e integration test-integration
Simulated inputs are generated at test time and cached under .cache/integration-sim/.
See docs/integration-tests.md for the scenario format and harness contract.
License
snippy-ng is distributed under the terms of the MIT license.
Funding
This work was funded by the CZI EOSS scheme from 2024-2026.
Authors
- Wytammma Wirth
- Torsten Seemann
1 maintainer
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