Minimap2 Module Documentation

Minimap2 is a pairwise sequence alignment algorithm designed for efficiently comparing nucleotide sequences. The algorithm uses a versatile indexing strategy to quickly find approximate matches between sequences, allowing it to efficiently align long sequences against reference genomes or other sequences.

Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34(18), 3094-3100.

ensembl.tools.anno.transcriptomic_annotation.minimap.run_minimap2(output_dir: Path, long_read_fastq_dir: Path, genome_file: Path, minimap2_bin: Path = PosixPath('minimap2'), paftools_bin: Path = PosixPath('paftools.js'), max_intron_length: int = 100000, num_threads: int = 1) → None

Run Minimap2 to align long read data against genome file. Default Minimap set for PacBio data.

param output_dir:

Working directory path.

type output_dir:

Path

param long_read_fastq_dir:

Long read directory path.

type long_read_fastq_dir:

Path

param genome_file:

Genome file path.

type genome_file:

Path

param minimap2_bin:

Software path.

type minimap2_bin:

Path, default minimap2

param paftools_bin:

Js path.

type paftools_bin:

Path, default paftools.js

param max_intron_length:

The maximum intron size for alignments. Defaults to 100000.

type max_intron_length:

int, default 100000

param num_threads:

Number of available threads.

type num_threads:

int, default 1

return:

None

rtype:

None