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SeqNado

Welcome to SeqNado! SeqNado is a powerful bioinformatics tool designed to simplify the analysis and integration of high-throughput sequencing data. It supports a wide range of sequencing assays and provides advanced features for multiomics data processing.

Key Features

  • Multiomics Data Processing: Analyze and integrate data from multiple omics layers.
  • Configurable Workflows: Predefined workflows for ATAC, ChIP, RNA, and more.
  • Third-Party Tool Integration: Seamless integration with popular bioinformatics tools.
  • Advanced Data Processing: Includes features like spike-in normalization, blacklist removal, and genome tiling.

Supported Assays

SeqNado supports the following sequencing assays:

  • RNA-seq: Transcriptome analysis.
  • ATAC-seq: Chromatin accessibility profiling.
  • SNP Analysis: Single nucleotide polymorphism detection.
  • ChIP-seq: Protein-DNA interaction analysis.
  • CUT&Tag: Epigenomic profiling.
  • Methylation: DNA methylation analysis.
  • MCC: Multiplex chromatin conformation capture.
  • CRISPR: CRISPR screening analysis.

Use Cases

SeqNado is ideal for:

  • Researchers analyzing high-throughput sequencing data.
  • Bioinformaticians integrating multiomics datasets.
  • Labs requiring reproducible and scalable workflows.

Additional Features

SeqNado includes the following advanced capabilities:

  • Spike-in Normalization: Calculate normalization factors for spike-in controls.
  • Data Visualization: Generate publication-ready plots and figures.
  • UCSC Hub Generation: Create UCSC genome browser hubs for data sharing.
  • Genome Browser Plots: Generate visualizations for genome-wide data, including UCSC genome browser hubs.
  • Quantification Methods: Comprehensive tools for read count quantification, grouped read counts, and combined read counts.
  • Machine Learning Dataset Creation: Prepare datasets for machine learning applications.

These features are fully customizable through configuration files, making SeqNado adaptable to a variety of research needs.

Get Started

Follow the step-by-step guide to get up and running:

  1. Installation: Set up the SeqNado environment.
  2. Initialisation: Configure your local environment (CLI: seqnado init).
  3. Genome Setup: Manage reference genomes and indexes (CLI: seqnado genomes).
  4. Configuration: Define your experiment parameters (CLI: seqnado config).
  5. Design Guide: Create your sample metadata design (CLI: seqnado design).
  6. Pipeline Overview: Run the workflow (CLI: seqnado pipeline) and explore Outputs.

For a quick end-to-end example, see the Quick Start guide. - Pipeline