How do I install the Wgsim Eval Pl skill?

Run npx skillmds add vimalinx/wgsim-eval-pl 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 Wgsim Eval Pl safe to use?

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Which AI agents work with Wgsim Eval Pl?

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Is Wgsim Eval Pl free to use?

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

Who published Wgsim Eval Pl?

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

Wgsim Eval Pl by vimalinx — Agent Skill

Name: Wgsim Eval Pl
Rating: 4.2 (5 reviews)
Author: vimalinx

File contents

wgsim-eval-pl

Quick Start

Command: wgsim_eval.pl <command> [arguments]
Local executable: /home/vimalinx/miniforge3/envs/bio/bin/wgsim_eval.pl
Reference: See references/help.md for detailed usage

When To Use This Tool

Evaluate alignments or variant calls produced from wgsim-simulated data.
Compare aligner accuracy on SAM files whose read names encode wgsim truth.
Post-process SAM files to keep top-scoring hits before comparison.
Compare two unique-hit alignment outputs from competing mapping workflows.

Common Patterns

# 1) Summarize mapping accuracy from a wgsim-derived SAM file
wgsim_eval.pl \
  alneval \
  simulated.sam

# 2) Emit ROC-style alignment evaluation output
wgsim_eval.pl \
  alneval \
  -a \
  simulated.sam

# 3) Evaluate variant calls against wgsim SNP truth
wgsim_eval.pl \
  vareval \
  truth.wgsim.snp \
  calls.pileup.flt

# 4) Keep only the top-scoring SAM hit per read before downstream comparison
wgsim_eval.pl \
  unique \
  alignments.sam

Recommended Workflow

Decide which task you need: alneval, vareval, unique, or uniqcmp.
Confirm the inputs really come from wgsim-style simulations, because several subcommands depend on truth encoded in the read names or SNP truth files.
Run the chosen subcommand and capture the tabular output for downstream plotting or benchmarking.
If necessary, use unique before alneval or uniqcmp so multi-hit alignments are normalized consistently.

Guardrails

The first argument must be a subcommand; --help and --version are not recognized as top-level actions.
alneval and unique expect SAM alignments whose read names were generated by wgsim; generic SAM files can produce warnings or meaningless accuracy numbers.
vareval expects a wgsim.snp truth file plus a pileup-style variant call file.
unique and uniqcmp are alignment post-processing/evaluation helpers, not generic SAM validation commands.

---name: wgsim-eval-pldescription: Use when evaluating wgsim simulation results or analyzing simulated read data as part of samtools bioconda installations.--- # wgsim-eval-pl ## Quick Start - **Command:** `wgsim_eval.pl <command> [arguments]` - **Local executable:** `/home/vimalinx/miniforge3/envs/bio/bin/wgsim_eval.pl` - **Reference:** See [references/help.md](references/help.md) for detailed usage ## When To Use This Tool - Evaluate alignments or variant calls produced from `wgsim`-simulated data. - Compare aligner accuracy on SAM files whose read names encode wgsim truth. - Post-process SAM files to keep top-scoring hits before comparison. - Compare two unique-hit alignment outputs from competing mapping workflows. ## Common Patterns ```bash # 1) Summarize mapping accuracy from a wgsim-derived SAM file wgsim_eval.pl \ alneval \ simulated.sam ``` ```bash # 2) Emit ROC-style alignment evaluation output wgsim_eval.pl \ alneval \ -a \ simulated.sam ``` ```bash # 3) Evaluate variant calls against wgsim SNP truth wgsim_eval.pl \ vareval \ truth.wgsim.snp \ calls.pileup.flt ``` ```bash # 4) Keep only the top-scoring SAM hit per read before downstream comparison wgsim_eval.pl \ unique \ alignments.sam ``` ## Recommended Workflow 1. Decide which task you need: `alneval`, `vareval`, `unique`, or `uniqcmp`. 2. Confirm the inputs really come from `wgsim`-style simulations, because several subcommands depend on truth encoded in the read names or SNP truth files. 3. Run the chosen subcommand and capture the tabular output for downstream plotting or benchmarking. 4. If necessary, use `unique` before `alneval` or `uniqcmp` so multi-hit alignments are normalized consistently. ## Guardrails - The first argument must be a subcommand; `--help` and `--version` are not recognized as top-level actions. - `alneval` and `unique` expect SAM alignments whose read names were generated by `wgsim`; generic SAM files can produce warnings or meaningless accuracy numbers. - `vareval` expects a `wgsim.snp` truth file plus a pileup-style variant call file. - `unique` and `uniqcmp` are alignment post-processing/evaluation helpers, not generic SAM validation commands.

Frequently asked questions