Crystal Minimap2

A pure-Crystal port of minimap2. No C bindings, no FFI. Written using Claude Code.

Requirements

• Crystal >= 1.19.1

Build

make

Builds both bin/minimap2 and bin/paftools. Individual targets:

make minimap2
make paftools

Usage

bin/minimap2 -x map-ont ref.fa reads.fa
bin/minimap2 -x map-ont -c ref.fa reads.fa  # with CIGAR
bin/minimap2 -x map-ont -a ref.fa reads.fa  # SAM output
bin/minimap2 -x map-ont -t 8 ref.fa reads.fa
bin/minimap2 -d ref.mmi ref.fa              # build index
bin/minimap2 ref.mmi reads.fa              # map against index

Presets: map-ont, map-pb, map-hifi, asm5, asm10, asm20, splice, sr, ava-ont, ava-pb

paftools

bin/paftools <command> [options] <input>
bin/paftools <command> -h

Limitations

• No paired-end mode
• No split index for very large references
• Single-threaded index loading from .mmi files

Tests

make spec

License

This is a reimplementation of minimap2. The original license applies to the algorithms and design. This code is additionally licensed under MIT.