Skills Marketplace

Overview

BioContext7 skills are pre-built workflow templates that encode best practices for common bioinformatics tasks. Each skill combines tool discovery, pipeline generation, and validation into a single command.

Auto-Generated Skills

BioContext7 auto-generates SKILL.md files for the top 500 tools ranked by bc7score. These skills are generated from the unified registry and include tool descriptions, EDAM annotations, install commands, and usage patterns. The find-skills MCP tool searches across all 47K+ tools using semantic matching to surface the most relevant skills for any bioinformatics task.

Use the find-skills MCP tool to discover skills programmatically:

find-skills(task_description="single-cell RNA-seq clustering", top_k=5, compact=true)

Available Skills

RNA-seq Analysis

bc7 skill run rna-seq --input ./fastq/ --target nextflow

Generates a complete RNA-seq pipeline:

• Quality control (FastQC, MultiQC)
• Adapter trimming (Trim Galore)
• Alignment (STAR)
• Quantification (featureCounts)
• Differential expression (DESeq2)

Variant Calling

bc7 skill run variant-calling --input ./bam/ --target nextflow

Generates a variant calling pipeline:

• BAM preprocessing (Picard MarkDuplicates)
• Variant calling (GATK HaplotypeCaller)
• Variant filtering (GATK VQSR)
• Annotation (SnpEff)

ChIP-seq Peak Calling

bc7 skill run chip-seq --input ./fastq/ --target snakemake

Generates a ChIP-seq analysis pipeline:

• Read alignment (Bowtie2)
• Peak calling (MACS2)
• Motif analysis (HOMER)
• Quality metrics (deepTools)

Metabolomics

bc7 skill run metabolomics --input ./mzml/ --target nextflow

Generates a metabolomics data processing pipeline:

• Peak detection (XCMS)
• Alignment and grouping
• Metabolite identification (HMDB, MassBank)
• Statistical analysis

List Available Skills

bc7 skill list

Skill Parameters

Each skill accepts common parameters:

Creating Custom Skills

Create a skill definition in YAML:

name: my-custom-skill
description: Custom analysis workflow
steps:
  - name: qc
    tool: fastqc
    operation: quality_control
  - name: align
    tool: star
    operation: alignment
    depends_on: [qc]
  - name: count
    tool: featurecounts
    operation: quantification
    depends_on: [align]

Register the skill:

bc7 skill register ./my-skill.yaml