Sequelizer

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Nanopore bioinformatics for edge computing

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About

Analyze DNA sequences in real-time, on-device, across the edge network.

Sequelizer brings efficient bioinformatics to embedded sequencers, smartphones, and edge servers - processing nanopore data streams as they're generated, not hours later in the cloud.

Main Sequelizer documentation page (under construction)

Installation

Required:

# macOS
brew install argp-standalone hdf5
# Ubuntu/Debian (may need to drop libargp-dev if argp functionality is already built-in)
sudo apt-get update && sudo apt-get install -y libhdf5-dev libopenblas-dev pkg-config libcunit1-dev libargp-dev 
# Build tools
# CMake 3.23+ and C++17 compiler required

Optional (for testing):

# For plotting capabilities
brew install gnuplot feedgnuplot    # macOS
sudo apt-get install gnuplot        # Ubuntu
# For unit tests
brew install cunit                  # macOS
sudo apt-get install libcunit1-dev  # Ubuntu

Build

mkdir build && cd build
cmake .. && cmake --build .
cd ..  # Return to sequelizer directory

Quick Start

Run commands from the sequelizer/ directory (not build/):

# Analyze Fast5 files
./build/sequelizer fast5 data.fast5 --recursive --verbose

# Convert to text format
./build/sequelizer convert data.fast5 --to raw

# Plot signals
./build/sequelizer plot signals.txt

# Generate sequences (requires kmer_models/)
./build/sequelizer seqgen -M

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Full Documentation • Getting Started • Command Reference • Fast5 Compatibility