bwa-rustBWA in Rust

High-Performance · Memory-Safe · Zero Unsafe | Modern bioinformatics tool inspired by BWA-MEM

🚀 Get Started

📖 Documentation

💻 GitHub

🧬

FM Index

Suffix Array + BWT + Sparse SA Sampling, single .fm file with magic number

🎯

BWA-MEM Style

SMEM seeds → Chain building → Banded Smith-Waterman → Semi-global refinement

📄

SAM Output

Full @HD/@SQ/@PG headers, CIGAR, MAPQ, AS/XS/NM tags, SAM compliant

⚡

Multi-threaded

Rayon-based read-level parallelism with custom thread pool

🛡️

Memory Protection

max_occ / max_chains / max_alignments limits prevent memory explosion

🦀

Rust Safety

Zero unsafe code with compile-time safety guarantees

100%

Test Coverage

Unsafe Code

32+

Max Threads

⚡

O(n log²n)

SA Build

🎯

BWA-MEM

Style

🦀

Zero unsafe

Memory Safe

🔄 Alignment Pipeline

🧬

Read FASTQ

→

🎯

SMEM Seeds

→

🔗

Chain

→

✂️

SW Align

→

📄

SAM Output

💻 One Command Start

Build indexAlign reads

bash

# Build FM index from FASTA reference
bwa-rust index reference.fa -o ref

bash

# BWA-MEM style one-step alignment
bwa-rust mem ref.fa reads.fq -t 8 -o output.sam

📊 Comparison with BWA

Feature

BWA (C)

bwa-rust

Index Format

Multiple files

Single .fm file

Memory Safety

unsafe C code

🦀 Zero unsafe

Parallel

pthread

rayon (Rust)

Build Time

Fast (O(n))

Good (O(n log²n))

✅168 Tests Passing

🚀GitHub Actions CI

📦Cross-Platform

🌐Bilingual Docs