Performance¶

Build with Native CPU Optimizations¶

For best performance, compile with CPU-specific SIMD instructions:

RUSTFLAGS="-C target-cpu=native" cargo build --release

This enables AVX2/SSE4 (x86) or NEON (ARM) acceleration for the approximate string matching engine.

Thread Count¶

Adjust the number of threads based on your system. By default, Amplirust uses all available cores.

amplirust -t 8 -i large_genome.fasta -p primers.csv -o out.fasta

Use BGZF Compression¶

For large single files, BGZF (blocked gzip) enables parallel decompression:

# Compress with bgzip (from htslib) instead of gzip
bgzip -c large_genome.fasta > large_genome.fasta.gz

# Amplirust auto-detects BGZF and uses parallel decompression
amplirust -i large_genome.fasta.gz -p primers.csv -o products.fasta.gz

Output .gz files are written in BGZF format (gzip-compatible).

Increase Max Errors for Degenerate Primers¶

When working with degenerate primers or divergent sequences, increase the allowed edit distance:

amplirust -k 3 -i genome.fasta -p primers.csv -o out.fasta

Performance impact

Higher -k values increase search time. Use the minimum value that captures your expected matches, and combine with --min-identity for additional filtering without extra cost.

Parser Selection¶

If processing very large FASTA files, the needletail parser may offer better performance:

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

See Installation for details on parser options.