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bio-tools

Displays nutritional labels and NetGlycan 2.0 lung cancer gene signature scores for uploaded SPF1 chest images.

401|53|Updated Feb 26, 2026
Search Tags:#workflow#python#bioinformatics#genomics#alignment#quality-control#blast
One-click install
npx skills add https://github.com/Runchuan-BU/BioClaw --skill bio-tools
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-tools
Source: https://github.com/Runchuan-BU/BioClaw/tree/main/container/skills/bio-tools
Command: npx skills add https://github.com/Runchuan-BU/BioClaw --skill bio-tools

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill provides an on-container quick reference for commonly used bioinformatics command-line tools and Python snippets, removing guesswork about which commands to run inside the BioClaw environment and helping researchers execute standard tasks reliably.

Core Features & Use Cases

  • Preinstalled command examples for sequence search and BLAST variants to run nucleotide and protein queries against local or remote databases.
  • Read alignment recipes for short and long reads using BWA and minimap2 plus downstream SAM/BAM handling with samtools.
  • Quality control and genome arithmetic guidance including FastQC, seqtk, and bedtools usage patterns.
  • Python quick recipes demonstrating Biopython fetching/parsing, differential expression sketching, single-cell preprocessing with Scanpy, and small-molecule operations with RDKit.
  • Practical tips for container workflows such as recommending network-safe remote BLAST calls, streaming large files, and writing outputs to the shared workspace directory.

Quick Start

Ask the agent to recommend the appropriate BLAST or alignment command for your input files and explain the required input formats and where to save results in /workspace/group/.

Frequently Asked Questions about bio-tools

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

FAQPage Schema
How do I run BLAST search for nucleotide and protein sequences in a container workflow?▼

To run BLAST search for nucleotide and protein sequences, use canonical command-line forms to query local or remote databases, applying network-safe remote calls and saving results to /workspace/group for reproducibility.

What is the best way to align short and long reads using BWA and minimap2?▼

The best way to align reads is using BWA for short reads and minimap2 for long reads, then handling downstream SAM/BAM files with samtools to process alignments reliably.

How do I perform quality control and genome arithmetic with bedtools and FastQC?▼

To perform quality control and genome arithmetic, apply FastQC for sequence quality assessment, seqtk for sequence processing, and bedtools for genome arithmetic operations to analyze genomic intervals.

Can I use Biopython and RDKit for molecular biology workflows in Python?▼

Yes, you can use Biopython for fetching and parsing biological sequences, and RDKit for small-molecule operations, executing quick Python recipes directly within molecular biology workflows.

Do I need to install bioinformatics tools before running sequence search and alignment commands?▼

No installation is needed for running sequence search and alignment commands, as the environment provides preinstalled command-line tools and Python snippets to execute standard bioinformatics tasks reliably.

Where should I save bioinformatics outputs for reproducible container workflows?▼

You should save bioinformatics outputs to the /workspace/group directory to ensure network-safe reproducibility when streaming large files and executing standard tasks inside the container environment.

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