GeneWeaver: Parametric DNA Sequence Alignment Module in Chisel

GeneWeaver is a hardware design project developed in Chisel (Constructing Hardware in a Scala Embedded Language). It implements a fully parametric, hardware-accelerated Needleman-Wunsch algorithm for DNA sequence alignment, designed for flexibility, efficiency, and clarity.

Overview

This project simulates a matrix of ScoreCell modules that align two DNA sequences using customizable match/mismatch/gap scoring. It supports optional traceback for alignment reconstruction and offers two modes of operation: memory-mapped and streaming.

Key Features

• Modular hierarchy: ScoreCell, ScoreMatrix, and testbenches
• Parametric matrix size and scoring values
• Optional traceback reconstruction
• Streaming or memory-mapped I/O interface
• Verilog generation with ScoreMatrixGenerator.scala

---

Project Structure

GeneWeaver/
├── build.sbt
├── src/
│   ├── main/
│   │   └── scala/
│   │       ├── ScoreCell.scala              # Basic scoring unit for DNA pairwise comparison
│   │       ├── ScoreMatrix.scala            # Configurable matrix of ScoreCells
│   │       └── ScoreMatrixGenerator.scala   # Generator script for Verilog
│   └── test/
│       └── scala/
│           ├── ScoreCellTester.scala        # Tests for ScoreCell logic
│           ├── ScoreMatrixMemoryTester.scala # Tests matrix with memory-mapped I/O
│           └── ScoreMatrixStreamTester.scala # Tests matrix with streaming I/O

---

How to Run

Prerequisites

• Java (JDK 8+)
• sbt (Scala Build Tool)
• Internet (for fetching Chisel dependencies)

Run Tests

sbt test

Generate Verilog

sbt "runMain ScoreMatrixGenerator"

This generates the Verilog output for a configurable instance of the ScoreMatrix module.

---

Module Descriptions

ScoreCell.scala

A single comparison unit computing alignment scores between DNA bases. Accepts three directions (diag, up, left) and outputs the best score and traceback direction.

ScoreMatrix.scala

Constructs a parametric matrix of ScoreCells, processes two input sequences, and optionally reconstructs alignment via traceback.

ScoreMatrixGenerator.scala

Generates Verilog from a custom configuration of the ScoreMatrix.

ScoreCellTester.scala

Unit tests for standalone ScoreCell behavior.

ScoreMatrixMemoryTester.scala and ScoreMatrixStreamTester.scala

Test the matrix behavior using two different I/O styles — memory-mapped and streaming.

---

License

This project is for academic use and learning purposes.