Crystal Minimap2

A complete Crystal implementation of minimap2 — a versatile pairwise sequence aligner for nucleotide sequences. All algorithms are implemented directly in Crystal with no C bindings.

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 in PAF
bin/minimap2 -x map-ont -a ref.fa reads.fa     # SAM output
bin/minimap2 -x map-ont --cs ref.fa reads.fa   # cs tag (short form)
bin/minimap2 -x map-ont --MD -a ref.fa reads.fa # SAM with MD tag
bin/minimap2 -x map-ont -t 8 ref.fa reads.fa  # 8 threads
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, splice:hq, splice:sr, sr, ava-ont, ava-pb

Key options

paftools

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

Limitations

• No SIMD acceleration (scalar int32 alignment; slower than C for large alignments)
• No split index for very large references (index is built in memory)
• 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.