genomics-assembly

Name: genomics-assembly
Availability: InStock
Author: TianGzlab

Assemble genomes de novo with SPAdes, Megahit, Flye, or Canu and report N50, N90, and GC content.

155|26|Updated Mar 14, 2026

Search Tags:#bioinformatics #genomics #assembly #genome sequencing #SPAdes #Flye

Ready to run

npx skills add https://github.com/TianGzlab/OmicsClaw --skill genomics-assembly

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: genomics-assembly
Source: https://github.com/TianGzlab/OmicsClaw/tree/main/skills/genomics/genomics-assembly
Command: npx skills add https://github.com/TianGzlab/OmicsClaw --skill genomics-assembly

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires numpy, pandas, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the complex and memory-intensive process of de novo genome assembly, providing quality assessment metrics and wrapping popular assemblers.

Core Features & Use Cases

Automated Assembly: Wraps SPAdes, Megahit, Flye, and Canu for de novo genome assembly from short and long reads.
Quality Assessment: Calculates essential metrics like N50, N90, L50, L90, GC content, and contig length distribution, compatible with QUAST.
Use Case: Assemble a newly sequenced bacterial genome using long reads with Flye, then assess the assembly quality and completeness.

Quick Start

Assemble the provided genome reads using the genomics-assembly skill with the Flye assembler.

Frequently Asked Questions about genomics-assembly

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I perform de novo genome assembly from raw sequencing reads?▼

De novo genome assembly reconstructs contigs directly from short or long reads. This Skill automates the process using assemblers like SPAdes, Megahit, Flye, and Canu, generating contigs and reporting quality metrics.

Can I assemble a bacterial genome using long reads with Flye?▼

Yes, you can assemble a bacterial genome using long reads with Flye. The Skill wraps Flye and other assemblers to automate de novo genome assembly and then evaluates assembly quality and completeness.

What metrics are used for genome assembly quality assessment?▼

Genome assembly quality assessment uses metrics like N50, N90, L50, L90, GC content, and contig length distribution. This Skill calculates these metrics comprehensively, remaining compatible with QUAST standards.

Does this genome assembly Skill support short reads from SPAdes and Megahit?▼

Yes, this genome assembly Skill supports short reads by wrapping SPAdes and Megahit. It standardizes the process of generating contigs from short reads while providing comprehensive quality assessment metrics.

What's the best way to assess assembly completeness after generating contigs?▼

The best way to assess assembly completeness is by evaluating N50, N90, and GC content. This Skill automatically calculates these essential metrics and contig length distributions immediately after generating the assembly.

Why does de novo genome assembly require memory-intensive processes?▼

De novo genome assembly requires memory-intensive processes because it reconstructs large genomes from fragmented reads without a reference. This Skill automates these complex computations using assemblers like Canu and Flye.