Minimap#
Minimap2 is a pairwise sequence alignment algorithm designed for
API#
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.
References
[11]
- ensembl.tools.anno.transcriptomic_annotation.minimap.run_minimap2(output_dir, long_read_fastq_dir, genome_file, minimap2_bin=PosixPath('minimap2'), paftools_bin=PosixPath('paftools.js'), max_intron_length=100000, num_threads=1)[source]#
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