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Quick Start

Get started with SeqNado in just a few steps.

Tip

For a complete reference of all CLI commands and options, see the CLI Reference. This page provides detailed examples and common workflows.

SeqNado can be run for any of the following assay types, as well as in multiomics mode:

  • ATAC-seq: atac
  • ChIP-seq: chip
  • CUT&Tag: cat
  • RNA-seq: rna
  • Methylation: meth
  • SNP analysis: snp
  • MCC: mcc
  • CRISPR analysis: crispr

Example Workflow

1. Install SeqNado

The fastest method to install SeqNado is from bioconda via mamba.

mamba create -n seqnado -c bioconda seqnado
mamba activate seqnado

2. Initialise SeqNado

The seqnado init command initializes the SeqNado user environment. This step ensures that the necessary configuration files and dependencies are set up for the package to function correctly.

Usage

seqnado init [OPTIONS]

Options

  • --preset, --no-preset: Use packaged preset genomes instead of the editable template (default: disabled).
  • --dry-run, --no-dry-run: Show actions without writing files or running scripts (default: disabled).
  • --verbose, -v: Increase logging verbosity.

Actions Performed

  • Logs the current Conda environment if active (optional).
  • Runs the packaged Apptainer/Singularity initialization if apptainer is available on the system PATH.
  • Ensures the ~/.config/seqnado/genome_config.json file exists, either as a template or using a preset.

Example

Initialize SeqNado with default settings: 

seqnado init

For more details, see seqnado init.

3. Set up genome references for SeqNado

The seqnado genomes command manages genome configurations, including listing, editing, building, or generating fastq-screen configurations.

Usage

seqnado genomes [OPTIONS] SUBCOMMAND ASSAY

Subcommands

  • list: List available genome configurations.
  • edit: Edit an existing genome configuration.
  • build: Build a new genome configuration from a FASTA file.
  • fastqscreen: Generate a fastq-screen configuration file.

Arguments

  • SUBCOMMAND: The operation to perform (e.g., list, edit, build, fastqscreen).
  • ASSAY: Assay type. Options include rna, atac, snp, chip, cat, meth, mcc, crispr (default: atac).

Options

  • --fasta, -f: Input FASTA file (required for build).
  • --name, -n: Genome name (prefix) for the built genome.
  • --outdir, -o: Output directory for genome builds.
  • --screen, -s: Output path for fastq-screen configuration files (used in the fastqscreen subcommand).
  • --threads, -t: Number of threads for Bowtie2 (default: 8).
  • --no-contaminants: Exclude contaminant databases in fastq-screen configurations.
  • --contaminant-path: Path to contaminant reference files.
  • --verbose, -v: Increase logging verbosity.

Example

Build a genome configuration for RNA-seq: 

seqnado genomes build rna --fasta hg38.fasta --name hg38 --outdir /path/to/output

For more details, see seqnado genomes.

4. Configure a SeqNado run

The seqnado config command builds a workflow configuration YAML for the selected assay. If no assay is provided, the command operates in multiomics mode.

Usage

seqnado config [OPTIONS] [ASSAY]

Arguments

  • ASSAY: Assay type. Options include rna, atac, snp, chip, cat, meth, mcc, crispr. If omitted, multiomics mode is used.

Options

  • --make-dirs, --no-make-dirs: Create or skip creating the output project directory or FASTQ subdirectory (default: create).
  • --render-options, --no-render-options: Render all options, even if not used by the workflow (default: disabled).
  • --output, -o: Specify the explicit path for the rendered configuration file.
  • --interactive, --no-interactive: Enable or disable interactive prompts for configuration values (default: enabled).
  • --verbose, -v: Increase logging verbosity.

Example

Generate a configuration file: 

seqnado config atac

You can edit the generated YAML file to customize the workflow for your specific needs.

For more details, see seqnado config.

5. Generate experiment design

The seqnado design command generates a metadata design CSV from FASTQ files for a specific assay. If no assay is provided, the command operates in multiomics mode. The generated CSV outlines the structure of the experiment, including sample names, conditions, and other relevant metadata.

Usage

seqnado design [OPTIONS] [ASSAY] [FASTQ ...]

Arguments

  • ASSAY: Assay type. Options include rna, atac, snp, chip, cat, meth, mcc, crispr. If omitted, multiomics mode is used.
  • FASTQ: One or more FASTQ files to include in the design.

Options

  • --output, -o: Specify the output CSV filename (default: metadata_{assay}.csv).
  • --group-by: Group samples by a regular expression or a column.
  • --auto-discover: Automatically search common folders for FASTQ files if none are provided (default: enabled).
  • --interactive: Interactively add missing columns using schema defaults (default: enabled).
  • --accept-all-defaults: Non-interactive mode; auto-add only columns with schema defaults.
  • --verbose, -v: Increase logging verbosity.

Example

Generate a design CSV for ATAC-seq: 

seqnado design atac

The generated CSV can be reviewed and edited to ensure all experimental details are correctly specified.

For more details, see seqnado design.

6. Run SeqNado pipeline

The seqnado pipeline command runs the data processing pipeline for the specified assay. It uses Snakemake under the hood to manage the workflow.

Usage

seqnado pipeline [OPTIONS] [ASSAY]

Arguments

  • ASSAY: Assay type. Required for single-assay workflows, optional for multiomics mode.

Options

  • --configfile: Path to a SeqNado configuration YAML file (default: config_<ASSAY>.yaml).
  • --preset: Snakemake job profile preset. Options include:
  • lc: Local cluster
  • le: Local execution (default)
  • ls: Local single-threaded
  • ss: SLURM scheduler
  • t: Test mode
  • --clean-symlinks, --no-clean-symlinks: Remove symlinks created by previous runs (default: disabled).
  • --scale-resources, -s: Scale memory and time resources (default: 1.0).
  • --verbose, -v: Increase logging verbosity.
  • --queue, -q: Specify the SLURM queue/partition for the ss preset (default: short).
  • --print-cmd: Print the Snakemake command before running it.

Examples

Run the pipeline locally for ATAC-seq: 

seqnado pipeline atac --preset le

Run on an HPC cluster with SLURM and increased resources: 

seqnado pipeline atac --preset ss --queue short --scale-resources 1.5

For more details, see seqnado pipeline or the HPC Clusters guide for cluster-specific configuration.