Clair3

The Snippy-NG installer does not include Clair3 by default because it is large. The Clair3 environment and models are roughly 800 MB, so long-read users need to choose how they want to provide it.

Snippy-NG uses Clair3 by calling run_clair3.sh. Any installation method is fine as long as a working run_clair3.sh command is available on PATH.

Option 1: Use FreeBayes

This is the simplest option and should run out of the box with the Snippy-NG installer:

snippy-ng long --ref reference.fasta --reads reads.fastq.gz --caller freebayes

This is not the preferred long-read caller, but it avoids the Clair3 dependency.

Option 2: Install Clair3 Separately

Create a conda environment with Clair3 installed:

conda create -n clair3 -c conda-forge -c bioconda -y clair3

Add a wrapper called run_clair3.sh to a directory on your PATH. This example assumes ~/.local/bin is already on your PATH:

cat << 'EOF' > ~/.local/bin/run_clair3.sh
#!/usr/bin/env bash

conda run -n clair3 run_clair3.sh "$@"
EOF

chmod u+x ~/.local/bin/run_clair3.sh

Check that Snippy-NG can find it:

which run_clair3.sh
run_clair3.sh --help

Then run Snippy-NG with the default long-read caller:

snippy-ng long --ref reference.fasta --reads reads.fastq.gz

Option 3: Use Docker

The repository includes a Docker wrapper for Clair3:

install -m 755 docs/installation/run_clair3_docker.sh ~/.local/bin/run_clair3.sh

The wrapper runs the Clair3 container and mounts directories for common Clair3 input and output arguments. By default it uses:

hkubal/clair3:latest

Override the image if needed:

export CLAIR3_DOCKER_IMAGE=hkubal/clair3:latest

On some platforms, you may also need to set a Docker platform:

export CLAIR3_DOCKER_PLATFORM=linux/amd64

Option 4: Install Snippy-NG With Clair3

You can manually create an environment that contains both Clair3 and the Snippy-NG Python package:

conda create -n clair3 -c bioconda clair3 pip
conda activate clair3
pip install snippy-nextgen

Then install any other external tools you need into the same environment. For example:

conda install -c bioconda minimap2 samtools bcftools bedtools freebayes

This works, but it is more manual than the Snippy-NG installer because you are responsible for filling in missing pipeline dependencies.

Clair3 Models

Snippy-NG can use Longbow to predict a Clair3 model for read input, but the model files still need to exist somewhere accessible.

Set a model root with either:

export CLAIR3_MODELS=/path/to/clair3_models
export CLAIR3_MODEL_ROOT=/path/to/clair3_models

Or pass a model directly:

snippy-ng long \
  --ref reference.fasta \
  --reads reads.fastq.gz \
  --clair3-model /path/to/model

When using BAM or CRAM input with Clair3, pass --clair3-model explicitly:

snippy-ng long \
  --ref reference.fasta \
  --bam reads.bam \
  --clair3-model /path/to/model

Future Conda Package

Once Snippy-NG is available as a conda package, the intended install path will be closer to:

conda create -n snippy-ng -c bioconda snippy-ng clair3

That package is not available yet.