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genome-assembly

Generate de novo genome assemblies from short and long reads with QC and contamination assessment.

25|5|Updated Mar 22, 2026
Search Tags:#scaffolding#bioinformatics#de novo#polishing#genome-assembly#contamination#assembly-quality
One-click install
npx skills add https://github.com/zongtingwei/Bioclaw_Skills_Hub --skill genome-assembly
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: genome-assembly
Source: https://github.com/zongtingwei/Bioclaw_Skills_Hub/tree/main/skills/genomics-and-variation/genome-assembly
Command: npx skills add https://github.com/zongtingwei/Bioclaw_Skills_Hub --skill genome-assembly

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Genome assembly workflows automate the creation of contiguous genome assemblies from sequencing reads, including scaffolding, polishing, contamination review, and QC reporting.

Core Features & Use Cases

  • De novo assembly: construct contigs/scaffolds from short, long, or hybrid reads.
  • Quality control and contamination checks: assess completeness and detect potential contamination.
  • Reproducible pipelines: provide runnable patterns for consistent results across projects.

Quick Start

Provide short and/or long reads (with optional reference) to run the genome assembly workflow and obtain assembled contigs plus QC reports.

Frequently Asked Questions about genome-assembly

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

FAQPage Schema
How do I run de novo genome assembly from short and long reads?▼

De novo genome assembly can be performed by providing short, long, or hybrid sequencing reads to generate contiguous contigs or scaffolds. The workflow outputs assembled sequences, QC metrics, and contamination summaries.

What is the best way to check assembly quality and detect contamination?▼

Assembly quality and contamination assessment are handled by evaluating completeness and detecting potential contaminants within the workflow. This process produces detailed QC reports and contamination summaries alongside the assembled contigs.

Can I use hybrid reads for scaffolding and polishing in a genome assembly workflow?▼

Yes, hybrid reads from short and long sequencing technologies are supported for scaffolding and polishing. The workflow constructs contiguous assemblies and generates reproducible Python-based toolchains for consistent results.

Do I need a reference genome to assemble contigs for non-model species?▼

A reference genome is optional for de novo assembly of non-model species. You only need to provide sequencing reads to generate assembled contigs, scaffolds, and associated quality control metrics.

What's the best way to ensure reproducible genome assembly pipelines across projects?▼

Reproducible genome assembly pipelines use runnable Python-based toolchains to maintain consistent results across multiple projects. This approach standardizes de novo assembly, scaffolding, polishing, and contamination review steps.

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