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A partial reimplementation of nsearch in Zig

This is a partial rewrite of nsearch from C++ into Zig, with the primary goal to learn Zig. Compared to the C++ version, this version offers a limited feature set, but with better performance.

  • Search only, no merge or filter capabilities
  • FASTA file support (no FASTQ, no gzip support for input)
  • ALNOUT file support
  • DNA/protein sequences are both supported

It's unlikely that this project will ever meet feature parity with the C++ version of (lib)nsearch.

Building

You only need Zig. Built in the project root folder with (-Drelease-fast is recommended for best performance, omit for debug).

zig build -Drelease-fast

The binary will be located in ./zig-out/bin/nsearchz

Usage example

./nsearchz --query /opt/data/query.fa  --db /opt/data/db.fa --out /tmp/results.alnout --min-identity 0.75 --max-hits 1 --max-rejects 8 --strand plus