dustmasker

name	dustmasker
description	Use when masking low-complexity regions in nucleotide sequences using the Symmetric DUST algorithm before BLAST searches or other sequence analyses.
disable-model-invocation	true
user-invocable	true

dustmasker

Quick Start

• Command: dustmasker -in input.fasta -out masked.out -outfmt fasta
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/dustmasker
• Version: BLAST+ 2.17.0+
• Full reference: See references/help.md

When To Use This Tool

• Mask low-complexity nucleotide regions before running BLAST or related seed-based searches.
• Produce interval masks, mask ASN.1/XML, or masked FASTA depending on downstream needs.
• Prepare masking information from FASTA or an existing nucleotide BLAST database.
• Prefer segmasker for protein low-complexity masking, not dustmasker.

Common Patterns

# 1) Emit interval-style mask coordinates
dustmasker \
  -in genome.fa \
  -out genome.mask.interval \
  -outfmt interval

# 2) Produce soft-masked FASTA for downstream nucleotide BLAST
dustmasker \
  -in genome.fa \
  -out genome.softmasked.fa \
  -outfmt fasta

# 3) Produce hard-masked FASTA with Ns in masked regions
dustmasker \
  -in genome.fa \
  -out genome.hardmasked.fa \
  -outfmt fasta \
  -hard_masking

Recommended Workflow

1. Decide whether downstream tools want interval masks, FASTA output, or mask metadata in ASN.1/XML.
2. Run with default DUST parameters first; only tune -window, -level, or -linker when the default masking is clearly too weak or too aggressive.
3. Use soft-masked FASTA for most BLAST workflows unless your pipeline explicitly requires hard masking.
4. Inspect the masked fraction before assuming the preprocessing improved search specificity.

Guardrails

• This tool is for nucleotide input only.
• The default output format is interval, not FASTA.
• -hard_masking only matters when you request FASTA output.
• If FASTA identifiers matter downstream, consider -parse_seqids so sequence IDs are interpreted correctly.