https://github.com/cepdnaclk/e19-4yp-risc-v-based-asip-for-accelerating-dna-sequence-alignment-on-embedded-systems
RISC-V based application-specific instruction set processor (ASIP) for Minimap2
https://github.com/cepdnaclk/e19-4yp-risc-v-based-asip-for-accelerating-dna-sequence-alignment-on-embedded-systems
asip bioinformatics-acceleration dna-sequence-alignment embedded-systems fpga genomic-computing hardware-acceleration minimap2 risc-v rocket-chip third-generation-sequencing
Last synced: 2 months ago
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RISC-V based application-specific instruction set processor (ASIP) for Minimap2
- Host: GitHub
- URL: https://github.com/cepdnaclk/e19-4yp-risc-v-based-asip-for-accelerating-dna-sequence-alignment-on-embedded-systems
- Owner: cepdnaclk
- Created: 2025-02-02T10:23:47.000Z (8 months ago)
- Default Branch: main
- Last Pushed: 2025-05-28T10:57:26.000Z (4 months ago)
- Last Synced: 2025-05-28T11:36:59.198Z (4 months ago)
- Topics: asip, bioinformatics-acceleration, dna-sequence-alignment, embedded-systems, fpga, genomic-computing, hardware-acceleration, minimap2, risc-v, rocket-chip, third-generation-sequencing
- Homepage: https://cepdnaclk.github.io/e19-4yp-RISC-V-Based-ASIP-for-Accelerating-DNA-Sequence-Alignment-on-Embedded-Systems/
- Size: 6.84 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Accelerating Minimap2 on Embedded Systems Using RISC-V Based ASIP
This repository accompanies the literature review and ongoing research into optimizing **Minimap2**, a widely used DNA sequence alignment tool, for **embedded systems** through the use of **RISC-V-based Application-Specific Instruction-set Processors (ASIPs)**. The project explores hardware acceleration of Minimap2's **chaining stage** using a custom co-processor integrated into the **Rocket Chip platform** via the **RoCC (Rocket Custom Coprocessor) interface**.
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## 🧬 Motivation
Third-generation DNA sequencing technologies, such as **Oxford Nanopore MinION**, enable portable real-time sequencing of long reads. While these technologies offer advantages in genome completeness and accuracy, they also pose serious **computational challenges**, particularly for **real-time and on-site processing**.
Minimap2 is considered the gold-standard tool for long-read alignment but is computationally demanding—especially its **chaining stage**. Most optimization efforts so far have targeted **HPC systems**. There's a lack of research into accelerating Minimap2 on **embedded platforms** where **energy-efficiency and hardware constraints** are critical.
This project aims to fill that gap.
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## 🎯 Objectives
- Review computational challenges in long-read DNA sequence alignment.
- Identify performance bottlenecks in Minimap2, particularly in the chaining stage.
- Explore hardware acceleration strategies for embedded systems using RISC-V.
- Design and simulate an ASIP via the RoCC interface to accelerate chaining.
- Evaluate performance improvements and resource utilization.
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## 🛠️ Technologies Used
| Technology | Description |
|--------------------|-------------------------------------------------------------|
| **Minimap2** | Long-read sequence aligner (baseline software) |
| **RISC-V** | Open ISA used for designing a custom ASIP |
| **Rocket Chip** | RISC-V SoC generator with RoCC interface |
| **RoCC** | Custom co-processor interface in Rocket Chip |
| **Verilog / Chisel** | HDL/DSL used for ASIP design |
| **FPGA / Simulation** | Optional future implementation for prototyping |
| **Linux / Ubuntu** | Target OS for embedded simulation and profiling |
---
## 📌 Current Status
- ✅ Literature review completed
- ✅ Performance bottleneck identified: chaining stage in Minimap2
- ⚙️ ASIP design under development
- 🔄 Integration with Rocket Chip via RoCC pending
- 📊 Benchmarking and validation planned
---
## 📈 Future Work
- Integrate ASIP with Rocket Chip SoC
- Profile energy and latency on embedded simulations
- Port to FPGA for real-world prototyping
- Extend support to more stages in Minimap2 (seeding, alignment)
- Publish findings in a peer-reviewed venue
---
## 📚 References
- [Minimap2: Pairwise alignment for long DNA sequences](https://doi.org/10.1093/bioinformatics/bty191)
- [Oxford Nanopore Technologies](https://nanoporetech.com/)
- [Rocket Chip Generator](https://github.com/chipsalliance/rocket-chip)
- Literature cited in the `docs/` folder
---
## 🧠 Acknowledgments
This research is conducted as part of ongoing academic efforts in **computational bioengineering** and **hardware-software co-design for genomics**.