snippy-nextgen 1.34.0

The Next Generation of Microbial Variant Calling with Snippy

Snippy-NG

🚨 Snippy-NG is under construction and should not replace Snippy 🚨

Find the Snippy-NG documentation at cpg.org.au/snippy-ng and follow our progress in the Snippy-NG Development Blog!

Table of Contents

• Installation
• License

Installation

snippy is available on PyPI and can be installed using pip (without external dependencies):

pip install snippy-nextgen

The complete snippy-ng environment (including most dependencies) can be installed using the snippy-ng installer script. This script will install the latest version of snippy-ng and all its dependencies.

curl -sSL https://cpg.org.au/snippy-ng/install.sh | bash -s -- --force

Examples

snippy-ng asm --ref tests/data/reference.gbk --asm tests/data/wildtype.contigs.fa

snippy-ng short --ref tests/data/reference.gbk --R1 tests/data/mutant_R1.fastq.gz --R2 tests/data/mutant_R2.fastq.gz

export CLAIR3_MODELS=./clair3_models # try to find appropriate models in this directory
snippy-ng long --ref tests/data/JKD6159.fasta --reads 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 [e-mail]: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.