Nextclade CLI

Nextclade is a tool that identifies differences between your sequences and a reference sequence, uses these differences to assign your sequences to clades, and reports potential sequence quality issues in your data. You can use the tool to analyze sequences before you upload them to a database, or if you want to assign Nextstrain clades to a set of sequences.

You can learn more about the algorithm in the Algorithm section.

This section describes:

how to install Nextclade CLI - using Docker container and natively
how to run Nextclade CLI with sample data
what other sections of the documentation are worth checking after that

Installation (with docker)

Container images are available at Docker Hub: 🐋 nextstrain/nextclade

Pull and run the latest version with:

docker pull nextstrain/nextclade:latest
docker run -it --rm nextstrain/nextclade:latest nextclade --help

Pull and run a specific version with:

docker run -it --rm nextstrain/nextclade:2.0.0 nextclade --help

⚠️Don’t forget to mount necessary docker volumes to be able to supply the data into the container and to access the results. You may want to also add --user argument to docker command, to run on behalf of a non-root user and group. This is not specific to Nextclade. Please refer to Docker documentation for more details.

Docker images are available based on:

debian (default): Nextclade executable + a set of basic Linux utilities, such as bash, curl and wget, to facilitate usage in workflows
alpine: pure Alpine + Nextclade executable
scratch: empty image + Nextclade executable

You can choose to use the latest available version (:latest or no tag), or to freeze a specific version (e.g. :2.0.0) or only major version (e.g. :2), or a base image (e.g. :debian) or both version and base image (e.g. :2.0.0-debian), or mix and match.

Tag :latest points to :debian.

Installation (local)

Download manually

You can download the latest version of Nextclade CLI for your platform using one of these direct links:

⬇️ nextclade for Linux (x86_64)
⬇️ nextclade for macOS (Intel, x86_64)
⬇️ nextclade for macOS (Apple Silicon, ARM64)
⬇️ nextclade for Windows (x86_64)

All versions and their release notes are available on 🐈 Github Releases.

These executables are self-contained and don’t require any dependencies. They can be renamed and moved freely. It is convenient to rename the executable to nextclade and to move to one of the directories included in system $PATH, so that it’s available from any directory in the console.

⚠️ Note that macOS executables are not currently signed with a developer certificate (it requires maintaining a paid Apple developer account). Recent versions of macOS might refuse to run the executable. Before invoking Nextclade on command line, follow these steps to add Nextclade to the exclude list: macOS User Guide: Open a Mac app from an unidentified developer, and check Security settings. Refer to the latest macOS documentation if none of this works.

⚠️ GNU vs musl. Nextclade has two flavors of executables for Linux: “gnu” and “musl”, depending on what libc is used. We recommend “gnu” flavor by default - it is typically faster. However, if for some reason “gnu” flavor does not work, try “musl”.

Download from command line

The following commands can be used to download Nextclade from command line, from shell scripts and inside dockerfiles:

🐧 Linux x86_64 (click to expand)

Download latest version:

curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-x86_64-unknown-linux-gnu" -o "nextclade" && chmod +x nextclade

Download specific version:

curl -fsSL "https://github.com/nextstrain/nextclade/releases/download/2.0.0/nextclade-x86_64-unknown-linux-gnu" -o "nextclade" && chmod +x nextclade

🍏 macOS Intel (click to expand)

Download latest version:

curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-x86_64-apple-darwin" -o "nextclade" && chmod +x nextclade

Download specific version:

curl -fsSL "https://github.com/nextstrain/nextclade/releases/download/2.0.0/nextclade-x86_64-apple-darwin" -o "nextclade" && chmod +x nextclade

🍎 macOS Apple Silicon (click to expand)

Download latest version:

curl -fsSL "https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-aarch64-apple-darwin" -o "nextclade" && chmod +x nextclade

Download specific version:

curl -fsSL "https://github.com/nextstrain/nextclade/releases/download/2.0.0/nextclade-aarch64-apple-darwin" -o "nextclade" && chmod +x nextclade

🪟 Windows x86_64 PowerShell (click to expand)

Download latest version:

Invoke-WebRequest https://github.com/nextstrain/nextclade/releases/latest/download/nextclade-x86_64-pc-windows-gnu.exe -O nextclade.exe

Download specific version:

Invoke-WebRequest https://github.com/nextstrain/nextclade/releases/download/2.0.0/nextclade-x86_64-pc-windows-gnu.exe -O nextclade.exe

Using conda

⚠️Note that new versions may appear on bioconda with some delay (hours to weeks)

A Nextclade conda package is available for Linux and macOS from the conda channel bioconda:

conda install -c bioconda nextclade

Usage

Refer to help prompt for usage of Nextclade:

nextclade --help

Each subcommand has its own help prompt:

nextclade dataset --help
nextclade dataset list --help
nextclade dataset get --help
nextclade run --help

Quick Example

Download SARS-CoV-2 dataset:
```
nextclade dataset get --name 'sars-cov-2' --output-dir 'data/sars-cov-2'
```
Observe downloaded dataset files in the directory data/sars-cov-2/

💡️ This command will download the latest SARS-CoV-2 dataset. You should run it periodically to update the dataset, in order to get the latest features, including the most up-to-date clade assignment. Find out more in the Nextclade datasets section.
Run using the downloaded dataset and its example sequences (data/sars-cov-2/sequences.fasta):
```
nextclade run \
   --input-dataset data/sars-cov-2 \
   --output-all=output/ \
   data/sars-cov-2/sequences.fasta
```
Try to provide your own data instead of data/sars-cov-2/sequences.fasta.

For more controls, specify input files explicitly and/or add more flags for output files:
```
nextclade run \
   --in-order \
   --input-dataset=data/sars-cov-2 \
   --input-ref=data/sars-cov-2/reference.fasta \
   --input-gene-map=data/sars-cov-2/genemap.gff \
   --genes=E,M,N,ORF1a,ORF1b,ORF3a,ORF6,ORF7a,ORF7b,ORF8,ORF9b,S \
   --input-tree=data/sars-cov-2/tree.json \
   --input-qc-config=data/sars-cov-2/qc.json \
   --input-pcr-primers=data/sars-cov-2/primers.csv \
   --input-virus-properties=data/sars-cov-2/virus_properties.json \
   --output-fasta=output/nextclade.aligned.fasta.gz \
   --output-json=output/nextclade.json \
   --output-ndjson=output/nextclade.ndjson \
   --output-csv=output/nextclade.csv \
   --output-tsv=output/nextclade.tsv \
   --output-tree=output/nextclade.auspice.json \
   --output-translations=output/gene_{gene}.translation.fasta.gz \
   data/sars-cov-2/sequences.fasta \
   my_sequences1.fasta.gz \
   my_sequences2.fasta.xz
```
Add --verbose flag to show more information in the console. Add --include-reference flag to also write gap-stripped reference sequence and reference peptides into outputs. Add --in-order to preserve the same order of results in output files as in input fasta (has runtime performance cost).

The --input-dataset flag can be combined with individual --input* flags. In this case, individual flags override the corresponding files in the dataset.

If --output-all is used, you can set the --output-basename to control filenames and --output-selection=all,fasta,json,ndjson,csv,tsv,tree,translations,insertions,errors to control which files are emitted.

There is even more advanced flags to control alignment and other parts of the algorithm. Refer to nextclade run --help for more details.

You can learn more about input and output files in sections: Input files, Output files and Nextclade datasets. Read the built-in help (nextclade --help) for the detailed description of each subcommand and each flag.
Find the output files in the output/ directory:

nextclade.aligned.fasta - aligned input sequences
nextclade_gene_<gene_name>.translation.fasta - aligned peptides corresponding to each gene
nextclade.insertions.csv - list of stripped insertions, for each input sequence
nextclade.tsv - results of the analysis in TSV format
nextclade.csv - same results, but in CSV format
nextclade.json - detailed results of the analysis in JSON format
nextclade.ndjson - detailed results of the analysis in newline-delimited JSON format
nextclade.auspice.json - same as input tree, but with the input sequences placed onto it
nextclade.errors.csv - list of errors, warnings and failed genes

What’s next?

Congratulations, You have learned how to use Nextclade CLI!

Going further, you might want to learn about the science behind the Nextclade internals in the Algorithm section. The required input data is described in Input files section. And produced files are described in Output files section. The datasets are described in more details in the Nextclade datasets section.

For a more convenient online tool, check out Nextclade Web.

Nextclade is an open-source project. We welcome ideas and contributions. Head to our GitHub repository if you want to obtain source code and contribute to the project.