bio-tools

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/.