Getting Started with Sequelizer

This guide will help you install Sequelizer and run your first commands.

Quick Start

Once you have Sequelizer built, here are the essential commands to get started:

# Build Sequelizer
mkdir build && cd build
cmake .. && cmake --build .

# Analyze Fast5 files
./sequelizer fast5 data.fast5
./sequelizer fast5 /path/to/dataset/ --recursive --verbose

# Extract raw signals
./sequelizer convert data.fast5 --to raw
./sequelizer convert /path/to/dataset/ --to raw --recursive --all

Installation and Build

Requirements

macOS Setup

# Install dependencies
brew install hdf5

# Build Sequelizer
mkdir build && cd build
cmake .. && cmake --build .

# Executable: build/sequelizer

Linux Setup

# Ubuntu/Debian
sudo apt-get install libhdf5-dev cmake

# CentOS/RHEL
sudo yum install hdf5-devel cmake

# Build
mkdir build && cd build
cmake .. && cmake --build .

Build Targets

First Steps

After building Sequelizer, try these commands:

1. Analyze a Fast5 File

# Single file analysis
./sequelizer fast5 data.fast5

# Dataset analysis with full details
./sequelizer fast5 /path/to/dataset/ --recursive --verbose

# Debug problematic files
./sequelizer fast5 problematic.fast5 --debug

2. Extract Raw Signals

# Convert single file to raw signals
./sequelizer convert data.fast5 --to raw

# Batch convert with all reads
./sequelizer convert /path/to/dataset/ --to raw --recursive --all --output signals/

3. Get Help

# General help
./sequelizer --help

# Command-specific help
./sequelizer fast5 --help
./sequelizer convert --help

Next Steps