A minimap2-based aligner with BINSEQ file format support (*.bq and *.vbq). For converting FASTQ to BINSEQ formats see bqtools.

This uses the minimap2-rs library which facilitates raw FFI bindings to the minimap2 C library.

mmr is written in rust and deployed with cargo.

# install binary from cargo
cargo install mmr

# validate installation
mmr --version

mmr follows the same (or similar) CLI as the original minimap2 binary.

# map a *.bq file
mmr -x map-pb <library.fa> <query.bq>

# map a *.vbq file
mmr -x map-pb <library.fa> <query.vbq>

# map a *.fq file (supports compressed FASTQ as well)
mmr -x map-pb <library.fa> <query.fq>