precellar.make_minimap2_index#

precellar.make_minimap2_index(fasta, output_index, *, preset='map-ont')#

Create a minimap2 index from a FASTA file.

This function creates a .mmi index file that can be used with the MINIMAP2 aligner. The index is created with k-mer and window sizes optimized for the selected preset.

Parameters:

  • fasta (Path) – File path to the FASTA file containing reference sequences.

  • output_index (Path) – File path for the output minimap2 index (.mmi file).

  • preset (str) –

    Optional preset to optimize index for specific read types: - Long Reads DNA Mapping:

    • ’map-ont’: Oxford Nanopore reads (default)

    • ’map-pb’: PacBio CLR reads

    • ’map-hifi’: PacBio HiFi reads

    • ’lr:hq’: Long reads, high quality

    • Spliced / RNA-seq Alignment: - ‘splice’: RNA-seq long reads - ‘splice:hq’: High-quality RNA-seq long reads - ‘splice:sr’: Short-read RNA-seq

    • Long Assembly to Reference Mapping: - ‘asm5’, ‘asm10’, ‘asm20’: Assembly alignment (5%, 10%, 20% divergence)

    • Short Reads Mapping: - ‘short’: Short single-end reads - ‘sr’: Short paired-end reads

    • All-vs-All Overlap Mapping: - ‘ava-pb’: PacBio all-vs-all overlap - ‘ava-ont’: ONT all-vs-all overlap

Examples

>>> from precellar import make_minimap2_index
>>> make_minimap2_index("genome.fa", "genome.mmi", preset="map-ont")
>>> # For RNA-seq
>>> make_minimap2_index("transcriptome.fa", "transcriptome.mmi", preset="splice")

See also

aligners.MINIMAP2

The aligner class that uses these indices

make_bwa_index

Create BWA-MEM2 index for short reads

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