bonefish aligns Oxford Nanopore reads (FASTQ, FASTA or dorado BAM) to a reference and writes SAM, PAF or a coordinate-sorted, indexed BAM. Genomic DNA uses minimap2's lr:hq seeding and scoring with cheaper chaining and alignment, validated against GIAB truth sets; direct RNA and cDNA (-x rna, -x cdna) use minimap2's spliced presets with faster intron alignment, validated against minimap2, GENCODE and simulated reads.