SeqNado¶

Seqnado Logo

SeqNado is a Snakemake-based workflow for ChIP-seq (with optional spike-in normalisation), ATAC-seq, RNA-seq, and short-read WGS SNP calling. It is designed to be modular, reproducible, and easy to deploy using Apptainer/Singularity containers. SeqNado provides end-to-end pipelines that take you from raw FASTQ files to publication-ready results with minimal setup.

Quick Start¶

Follow the steps below to spin up a working pipeline instance. Consult the installation page or other docs as needed.

1. Install SeqNado¶

mamba install -c bioconda seqnado

The installation guide covers alternative methods, optional dependencies, and troubleshooting tips.

2. Scaffold a working directory¶

seqnado-config [atac|chip|rna|snp]

This command creates a project directory and the configuration skeleton for the selected pipeline.

3. Stage input data¶

Place or symlink raw FASTQ files into the generated fastq/ folder.
Copy or create any additional resources (e.g., spike-in references) expected by your config.

ln -s /path/to/fastq/*.fastq.gz /path/to/working-directory/fastq/

4. (Optional) Supply a design file¶

If your samples follow SeqNado naming conventions, the design table is generated automatically. Otherwise, run:

cd /path/to/working-directory
seqnado-design [atac|chip|rna|snp]

5. Launch the workflow¶

cd /path/to/working-directory
seqnado [atac|chip|rna|snp] -c <cores> --preset [ss|ls] \
  --queue/-q [short|long] --scale-resource/-s <factor>

# Example
seqnado rna -c 8 --preset ss

Use --preset ss to submit jobs to the cluster (recommended) or --preset ls for local execution. Adjust --queue and --scale-resource to fit your environment. Additional usage details, presets, and pipeline-specific parameters are documented in docs/pipeline.md and the CLI help (seqnado --help).