bio-genome-assembly-assembly-polishing

bio-genome-assembly-assembly-polishing is a skill for Claude Code, Codex from FridrichMethod/awesome-skills. It costs 190 tokens per session (5,153 once invoked), scanned A, original, no licence file.

A guide for improving a draft genome assembly's consensus accuracy using sequencing-read-specific polishing tools. Polishing corrects likely base and small sequence errors after the initial DNA reconstruction.

In plain words
What is it for?
Use it to decide whether to polish an assembly and select tools such as Racon, medaka, Polypolish, pypolca, Pilon, NextPolish, or haplotype-aware methods.
Why use it?
It helps choose tools that match the available read type, such as Oxford Nanopore or Illumina data. This reduces the risk of applying an unsuitable polishing method.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit Use it to decide whether to polish an assembly and select tools such as Racon, medaka, Polypolish, pypolca, Pilon, NextPolish, or haplotype-aware methods.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/fridrichmethod/awesome-skills/assembly-polishing
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add FridrichMethod/awesome-skills --skill assembly-polishing
Clone the repo
git clone --depth 1 https://github.com/FridrichMethod/awesome-skills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for bio-genome-assembly-assembly-polishing

README.md
[![agentmods](https://agentmods.dev/badge/skills/fridrichmethod/awesome-skills/assembly-polishing.svg)](https://agentmods.dev/skills/fridrichmethod/awesome-skills/assembly-polishing)
Your own site
<a href="https://agentmods.dev/skills/fridrichmethod/awesome-skills/assembly-polishing"><img src="https://agentmods.dev/badge/skills/fridrichmethod/awesome-skills/assembly-polishing.svg" alt="Measured on agentmods" height="20"></a>
Per session 190 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 5,153 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00190 $0.05153
Opus 5 $0.00095 $0.02576
Sonnet 5 $0.00038 $0.01031
Haiku 4.5 $0.00019 $0.00515

Measured 4d ago against content hash 97f562a6e3a5, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-07, from the pricing page.

Security

Grade A, and why

bio-genome-assembly-assembly-polishing scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 4d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (examples/polish_assembly.sh), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/assembly-polishing/SKILL.md · 194 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 4d ago First seen · 194 lines · 190 tokens per session scan A 97f562a6e3a5

Subscribe to this mod's changes

bio-genome-assembly-assembly-polishing is a skill published in the GitHub repository FridrichMethod/awesome-skills (14 stars, last pushed yesterday), with no licence file. It adds 190 tokens to every session and 5,153 once invoked, about $0.0010 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

Related

Other skills, from other repositories

experiment-craft

Use this skill when the user wants to debug, diagnose, or systematically iterate on an experiment that already exists, or when they need a structured experiment log for tracking runs, hypotheses, failures, results, and next steps during active research. Apply it to underperforming methods, training that will not…

EvoScientist/EvoSkills · 172 tokens

nonlinear-solvers

Select and configure nonlinear solvers for f(x)=0 or min F(x). Use for Newton methods, quasi-Newton (BFGS, L-BFGS), Broyden, Anderson acceleration, diagnosing convergence issues, choosing line search vs trust region, and analyzing Jacobian quality.

beita6969/ScienceClaw · 63 tokens

numerical-stability

Analyze and enforce numerical stability for time-dependent PDE simulations. Use when selecting time steps, choosing explicit/implicit schemes, diagnosing numerical blow-up, checking CFL/Fourier criteria, von Neumann analysis, matrix conditioning, or detecting stiffness in advection/diffusion/reaction problems.

beita6969/ScienceClaw · 61 tokens

academic-paper-writer

Draft economics papers with proper structure and academic style.

brycewang-stanford/Auto-Empirical-Research-Skills · 14 tokens

analysis-workflow

Organize multi-step scientific analyses into reproducible, self-contained modules. Use for workflows such as QC→PCA→DEG→GSEA that produce scripts, inputs, figures, tables, and methods. Creates a stable module layout, records exact inputs/parameters/package and database versions in each module README, keeps large data…

xuzhougeng/wisp-science · 81 tokens

bear-counter

A literature search that finds real academic papers challenging a claim through opposing findings, limits, alternative explanations, methodological criticism, or failed replications.

xuzhougeng/wisp-science · 270 tokens