Red Module Documentation

Red is the first repeat-detection tool capable of labeling its training data and training itself automatically on an entire genome. Girgis, H.Z. Red: an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale. BMC Bioinformatics 16, 227 (2015). https://doi.org/10.1186/s12859-015-0654-5

ensembl.tools.anno.repeat_annotation.red.run_red(genome_file: Path, output_dir: Path, red_bin: Path = PosixPath('Red')) → str

Run Red on genome file

param genome_file:

Genome file path.

type genome_file:

Path

param output_dir:

Working directory path.

type output_dir:

Path

param red_bin:

Red software path.

type red_bin:

Path, default Red

return:

Masked genome file

rtype:

str