How do I install the Mask Fasta From Bed skill?

Run npx skillmds add vimalinx/mask-fasta-from-bed in your terminal (requires Node.js), paste this page's agent-chat prompt into Claude, Cursor, or any MCP-connected agent, or download the SKILL.md file and copy it into your agent's skills directory.

Is Mask Fasta From Bed safe to use?

This skill has not completed SkillMD's automated safety review yet. Capability flags: reads secrets. SkillMD never runs a skill's scripts for you; review the SKILL.md before installing.

Which AI agents work with Mask Fasta From Bed?

This skill is tagged as working with Claude Code, Claude.ai, OpenAI Codex. SKILL.md is an open format, so most agents that read a skills directory can load it too.

Is Mask Fasta From Bed free to use?

Yes. Installing skills from SkillMD is free, and the skill stays under its author's original license.

Who published Mask Fasta From Bed?

vimalinx (@vimalinx) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Mask Fasta From Bed by vimalinx — Agent Skill

Name: Mask Fasta From Bed
Rating: 4.666666666666667 (3 reviews)
Author: vimalinx

Mask Fasta From Bed

Use when you need to hard-mask or soft-mask regions in a FASTA file using BED, GFF, or VCF coordinates, such as repetitive elements, blacklist regions, or loci to exclude from sequence analysis.

vimalinx b6b9ff1 2 files · 4.0 KB Updated Sep 9, 2026 0 repo stars

File contents

mask-fasta-from-bed

Quick Start

Command: maskFastaFromBed -fi <input.fasta> -bed <intervals.bed> -fo <output.fasta>
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/maskFastaFromBed
Full reference: See references/help.md

When To Use This Tool

Hard-mask repetitive, blacklisted, or excluded regions in a FASTA with N or another replacement character.
Soft-mask regions by lowercasing the existing sequence with -soft.
Apply interval masks from BED, GFF, or VCF files to a reference or contig FASTA.
Produce a derived masked FASTA without changing the original source file.

Common Patterns

# 1) Hard-mask listed regions with Ns
maskFastaFromBed \
  -fi genome.fa \
  -bed blacklist.bed \
  -fo genome.masked.fa

# 2) Soft-mask repeats by converting bases to lowercase
maskFastaFromBed \
  -fi genome.fa \
  -bed repeats.bed \
  -fo genome.softmasked.fa \
  -soft

# 3) Hard-mask with a custom replacement character and full FASTA headers
maskFastaFromBed \
  -fi contigs.fa \
  -bed mask-regions.bed \
  -fo contigs.masked.fa \
  -mc X \
  -fullHeader

Recommended Workflow

Confirm the interval file uses the same sequence naming convention as the FASTA headers.
Choose hard masking (default), soft masking with -soft, or an alternate hard-mask character with -mc.
Write the result to a new FASTA via -fo and preserve the original FASTA as the unmasked source.
Spot-check a few loci to confirm the intended regions were masked and the header matching behaved as expected.

Guardrails

-fo is required; this tool does not modify the input FASTA in place.
Default behavior replaces masked sequence with uppercase N; -soft instead lowercases the original bases.
-mc changes the hard-mask character; it is not a substitute for -soft.
By default bedtools matches only the first token of a FASTA header; use -fullHeader when interval names must match the entire header line.
Prefer -h for help; GNU-style --help and --version emit wrapper errors before usage text.

---name: mask-fasta-from-beddescription: Use when you need to hard-mask or soft-mask regions in a FASTA file using BED, GFF, or VCF coordinates, such as repetitive elements, blacklist regions, or loci to exclude from sequence analysis.--- # mask-fasta-from-bed ## Quick Start - **Command**: `maskFastaFromBed -fi <input.fasta> -bed <intervals.bed> -fo <output.fasta>` - **Local executable**: `/home/vimalinx/miniforge3/envs/bio/bin/maskFastaFromBed` - **Full reference**: See `references/help.md` ## When To Use This Tool - Hard-mask repetitive, blacklisted, or excluded regions in a FASTA with `N` or another replacement character. - Soft-mask regions by lowercasing the existing sequence with `-soft`. - Apply interval masks from BED, GFF, or VCF files to a reference or contig FASTA. - Produce a derived masked FASTA without changing the original source file. ## Common Patterns ```bash # 1) Hard-mask listed regions with Ns maskFastaFromBed \ -fi genome.fa \ -bed blacklist.bed \ -fo genome.masked.fa ``` ```bash # 2) Soft-mask repeats by converting bases to lowercase maskFastaFromBed \ -fi genome.fa \ -bed repeats.bed \ -fo genome.softmasked.fa \ -soft ``` ```bash # 3) Hard-mask with a custom replacement character and full FASTA headers maskFastaFromBed \ -fi contigs.fa \ -bed mask-regions.bed \ -fo contigs.masked.fa \ -mc X \ -fullHeader ``` ## Recommended Workflow 1. Confirm the interval file uses the same sequence naming convention as the FASTA headers. 2. Choose hard masking (default), soft masking with `-soft`, or an alternate hard-mask character with `-mc`. 3. Write the result to a new FASTA via `-fo` and preserve the original FASTA as the unmasked source. 4. Spot-check a few loci to confirm the intended regions were masked and the header matching behaved as expected. ## Guardrails - `-fo` is required; this tool does not modify the input FASTA in place. - Default behavior replaces masked sequence with uppercase `N`; `-soft` instead lowercases the original bases. - `-mc` changes the hard-mask character; it is not a substitute for `-soft`. - By default bedtools matches only the first token of a FASTA header; use `-fullHeader` when interval names must match the entire header line. - Prefer `-h` for help; GNU-style `--help` and `--version` emit wrapper errors before usage text.

Frequently asked questions