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Installation

The easiest way to install Amplirust is via Bioconda:

conda install bioconda::amplirust

mamba install bioconda::amplirust

Pre-built binaries are available for Linux (x86_64, aarch64) and macOS (x86_64, aarch64).

Verify installation

amplirust --version

From Source

Requires Rust 1.85+ (2024 edition).

# Clone the repository
git clone https://github.com/erdikilic/amplirust.git
cd amplirust

# Build with SIMD optimizations (recommended)
RUSTFLAGS="-C target-cpu=native" cargo build --release

# The binary will be at target/release/amplirust

Quick Install

RUSTFLAGS="-C target-cpu=native" cargo install --path .

Native CPU optimizations

Always use RUSTFLAGS="-C target-cpu=native" when building from source. This enables AVX2/SSE4 (x86) or NEON (ARM) acceleration for the approximate string matching engine, providing significant performance improvements.

FASTA Parser Selection

Amplirust supports two FASTA parsers via feature flags:

Feature Parser Description
parser_seqio (default) seq_io Fast, well-tested, minimal allocations
parser_needletail needletail Very fast, used in production bioinformatics tools 
RUSTFLAGS="-C target-cpu=native" cargo build --release

RUSTFLAGS="-C target-cpu=native" cargo build --release \
  --no-default-features --features parser_needletail

RUSTFLAGS="-C target-cpu=native" cargo install --path . \
  --no-default-features --features parser_needletail