How do I install the Remove Dup skill?

Run npx skillmds add vimalinx/remove-dup 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 Remove Dup safe to use?

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

Which AI agents work with Remove Dup?

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 Remove Dup free to use?

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

Who published Remove Dup?

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

Remove Dup by vimalinx — Agent Skill

Name: Remove Dup
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

remove-dup

Subread binary for duplicate-read removal. It reads SAM or BAM, groups reads by mapped location, and drops every read at locations whose depth meets or exceeds the configured duplication threshold.

Quick Start

Command: removeDup -i <input.sam|bam> -o <output.bam>
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/removeDup
Default duplication cutoff: 10

When To Use This Tool

Removing dense duplicate alignments from mapped read files before downstream counting or QC
Applying a simple location-based duplication filter to SAM or BAM without marking duplicates first
Forcing SAM output with -S when a downstream step cannot read BAM
Running a quick Subread-native duplicate purge rather than a more feature-rich deduplication workflow

Common Patterns

# Write BAM output with the default cutoff
removeDup -i alignments.bam -o dedup.bam

# Tighten the removal threshold
removeDup -i alignments.sam -o dedup.bam -r 2

# Emit SAM instead of BAM
removeDup -i alignments.bam -o dedup.sam -S

Recommended Workflow

Start from a valid SAM or BAM alignment file.
Decide whether the default cutoff of 10 is acceptable; lower it only if you intentionally want aggressive pruning.
Write BAM by default, or add -S only when plain-text SAM is required downstream.
Inspect the summary banner or view the output with samtools view to confirm how many reads actually survived.

Guardrails

-h and --version are not true metadata/help switches; both are treated as invalid options, then the binary prints its usage banner and continues to complain about missing or invalid input.
In live testing, three reads at the same locus with -r 2 caused all three reads to be removed, confirming this tool drops the entire location bucket once the cutoff is reached.
The usage text says output is BAM unless -S is specified, even though the -o description loosely says “output SAM file.”
The tool requires -i and -o; invoking it without a real SAM/BAM input ends in ERROR: The input file is neither a BAM file nor a SAM file.
This is a blunt duplicate filter, not a marker: it does not preserve one representative read at over-threshold loci.

---name: remove-dupdescription: Use when removing duplicate alignments from SAM or BAM files with the Subread `removeDup` CLI and a location-count cutoff.--- # remove-dup Subread binary for duplicate-read removal. It reads SAM or BAM, groups reads by mapped location, and drops every read at locations whose depth meets or exceeds the configured duplication threshold. ## Quick Start - **Command:** `removeDup -i <input.sam|bam> -o <output.bam>` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/removeDup` - **Default duplication cutoff:** `10` ## When To Use This Tool - Removing dense duplicate alignments from mapped read files before downstream counting or QC - Applying a simple location-based duplication filter to SAM or BAM without marking duplicates first - Forcing SAM output with `-S` when a downstream step cannot read BAM - Running a quick Subread-native duplicate purge rather than a more feature-rich deduplication workflow ## Common Patterns ```bash # Write BAM output with the default cutoff removeDup -i alignments.bam -o dedup.bam ``` ```bash # Tighten the removal threshold removeDup -i alignments.sam -o dedup.bam -r 2 ``` ```bash # Emit SAM instead of BAM removeDup -i alignments.bam -o dedup.sam -S ``` ## Recommended Workflow 1. Start from a valid SAM or BAM alignment file. 2. Decide whether the default cutoff of `10` is acceptable; lower it only if you intentionally want aggressive pruning. 3. Write BAM by default, or add `-S` only when plain-text SAM is required downstream. 4. Inspect the summary banner or view the output with `samtools view` to confirm how many reads actually survived. ## Guardrails - `-h` and `--version` are not true metadata/help switches; both are treated as invalid options, then the binary prints its usage banner and continues to complain about missing or invalid input. - In live testing, three reads at the same locus with `-r 2` caused all three reads to be removed, confirming this tool drops the entire location bucket once the cutoff is reached. - The usage text says output is BAM unless `-S` is specified, even though the `-o` description loosely says “output SAM file.” - The tool requires `-i` and `-o`; invoking it without a real SAM/BAM input ends in `ERROR: The input file is neither a BAM file nor a SAM file.` - This is a blunt duplicate filter, not a marker: it does not preserve one representative read at over-threshold loci.

Frequently asked questions