[meta]
name = "repeatmasker"
category = "annotation"
description = "Screens DNA sequences for interspersed repeats, low-complexity regions, and transposable elements"
tags = ["repeat", "transposon", "annotation", "masking", "genome", "te", "line", "sine"]
author = "oxo-call built-in"
source_url = "https://www.repeatmasker.org/"

[context]
concepts = [
    "RepeatMasker identifies and masks transposable elements, repetitive DNA, and low-complexity regions.",
    "Use -species to specify the organism (e.g., human, mouse, arabidopsis) for the repeat database.",
    "Output: <input>.masked (hard-masked N), <input>.softmasked or use -xsmall for softmasked (lowercase).",
    "RepeatMasker uses RepBase and/or Dfam databases; Dfam is freely available.",
    "Use -pa N for parallel processing (N processes); -dir for output directory.",
    "Softmasking (lowercase) is preferred for gene prediction tools like AUGUSTUS, MAKER.",
    "RepeatMasker output .out file contains coordinates, family, class, and score for each repeat.",
    "bedtools intersect with the .out file can mask custom repeat annotations.",
]

pitfalls = [
    "RepeatMasker is slow for large genomes (plant/mammal) — use -pa for parallelization.",
    "-xsmall creates softmasked output (lowercase repeats); default creates hard-masked (N) output.",
    "The species parameter must match RepBase/Dfam species naming — check available species.",
    "Without -dir, output files go to the same directory as input — use -dir for clean organization.",
    "Gene prediction tools like AUGUSTUS need softmasked, not hard-masked input.",
    "RepeatMasker may need updated databases (Dfam/RepBase) — check database version before running.",
]

[[examples]]
task = "softmask repeats in a mammalian genome assembly"
args = "-species human -xsmall -pa 16 -dir repeatmasker_output/ genome.fasta"
explanation = "-species human; -xsmall softmasking (lowercase repeats); -pa 16 parallel; -dir output directory"

[[examples]]
task = "hard-mask repeats in a plant genome"
args = "-species arabidopsis -pa 8 -dir masked_output/ genome.fasta"
explanation = "default hard-masking with N; -species arabidopsis; -pa 8 for parallel processing"

[[examples]]
task = "mask repeats using a custom library"
args = "-lib custom_repeats.fasta -xsmall -pa 8 -dir custom_masked/ genome.fasta"
explanation = "-lib custom repeat library; useful when species-specific repeats are known"

[[examples]]
task = "mask only simple repeats and low-complexity regions"
args = "-noint -xsmall -pa 4 -dir simple_masked/ genome.fasta"
explanation = "-noint skips interspersed repeats (TEs); only masks simple repeats and low-complexity regions"
