Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when preparing Ribo-seq reads for downstream analysis of translation.

Preprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other small RNAs. Use when preparing small RNA-seq reads for downstream quantification or discovery analysis.

Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay triangulation, and radius-based connectivity for downstream spatial analyses. Use when building spatial neighborhood graphs.

Peptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spectra. Covers database searching, spectral library matching, and FDR estimation using target-decoy approaches.

Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are needed.

Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short reads to a reference genome.

Perform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. Use when processing raw immune repertoire sequencing data to identify clonotypes and their frequencies.

Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences, creating new sequence files, or outputting modified records.

End-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation.

End-to-end small RNA-seq analysis from FASTQ to differential miRNA expression. Use when analyzing miRNA, piRNA, or other small RNA sequencing data.

End-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoire sequencing data from bulk or single-cell experiments.

This skill should be used when the user asks to "calculate TAM", "determine SAM", "estimate SOM", "size the market", "calculate market opportunity", "what's the total addressable market", or requests market sizing analysis for a startup or business opportunity.

Manage track lifecycle: archive, restore, delete, rename, and cleanup

You are an expert error analysis specialist with deep expertise in debugging distributed systems, analyzing production incidents, and implementing comprehensive observability solutions.

You are an expert error analysis specialist with deep expertise in debugging distributed systems, analyzing production incidents, and implementing comprehensive observability solutions.

You are a code migration expert specializing in transitioning codebases between frameworks, languages, versions, and platforms. Generate comprehensive migration plans, automated migration scripts, and

You are an expert team communication specialist focused on async-first standup practices, AI-assisted note generation from commit history, and effective remote team coordination patterns.

You are a code education expert specializing in explaining complex code through clear narratives, visual diagrams, and step-by-step breakdowns. Transform difficult concepts into understandable explanations.

You are a dependency management expert specializing in safe, incremental upgrades of project dependencies. Plan and execute dependency updates with minimal risk, proper testing, and clear migration pa

Implement the minimal code needed to make failing tests pass in the TDD green phase.

Build robust backtesting systems for trading strategies with proper handling of look-ahead bias, survivorship bias, and transaction costs. Use when developing trading algorithms, validating strategies, or building backtesting infrastructure.

Profile and optimize Python code using cProfile, memory profilers, and performance best practices. Use when debugging slow Python code, optimizing bottlenecks, or improving application performance.

Master Godot 4 GDScript patterns including signals, scenes, state machines, and optimization. Use when building Godot games, implementing game systems, or learning GDScript best practices.

Master Python asyncio, concurrent programming, and async/await patterns for high-performance applications. Use when building async APIs, concurrent systems, or I/O-bound applications requiring non-blocking operations.

This skill should be used when the user asks to "analyze competitors", "assess competitive landscape", "identify differentiation", "evaluate market positioning", "apply Porter's Five Forces", or requests competitive strategy analysis.

Create distributable Python packages with proper project structure, setup.py/pyproject.toml, and publishing to PyPI. Use when packaging Python libraries, creating CLI tools, or distributing Python code.

Calculate portfolio risk metrics including VaR, CVaR, Sharpe, Sortino, and drawdown analysis. Use when measuring portfolio risk, implementing risk limits, or building risk monitoring systems.

You are a GitHub issue resolution expert specializing in systematic bug investigation, feature implementation, and collaborative development workflows. Your expertise spans issue triage, root cause an

Use this skill when creating, managing, or working with Conductor tracks - the logical work units for features, bugs, and refactors. Applies to spec.md, plan.md, and track lifecycle operations.

Master TypeScript's advanced type system including generics, conditional types, mapped types, template literals, and utility types for building type-safe applications. Use when implementing complex type logic, creating reusable type utilities, or ensuring compile-time type safety in TypeScript projects.

Use this skill when implementing tasks according to Conductor's TDD workflow, handling phase checkpoints, managing git commits for tasks, or understanding the verification protocol.

Master error handling patterns across languages including exceptions, Result types, error propagation, and graceful degradation to build resilient applications. Use when implementing error handling, designing APIs, or improving application reliability.

Expert in strict POSIX sh scripting for maximum portability across Unix-like systems. Specializes in shell scripts that run on any POSIX-compliant shell (dash, ash, sh, bash --posix).

Create employment contracts, offer letters, and HR policy documents following legal best practices. Use when drafting employment agreements, creating HR policies, or standardizing employment documentation.

Build production-ready monitoring, logging, and tracing systems. Implements comprehensive observability strategies, SLI/SLO management, and incident response workflows. Use PROACTIVELY for monitoring infrastructure, performance optimization, or production reliability.

Expert performance engineer specializing in modern observability, application optimization, and scalable system performance. Masters OpenTelemetry, distributed tracing, load testing, multi-tier caching, Core Web Vitals, and performance monitoring. Handles end-to-end optimization, real user monitoring, and scalability patterns. Use PROACTIVELY for performance optimization, observability, or scalability challenges.

Build read models and projections from event streams. Use when implementing CQRS read sides, building materialized views, or optimizing query performance in event-sourced systems.

Expert startup business analyst specializing in market sizing, financial modeling, competitive analysis, and strategic planning for early-stage companies. Use PROACTIVELY when the user asks about market opportunity, TAM/SAM/SOM, financial projections, unit economics, competitive landscape, team planning, startup metrics, or business strategy for pre-seed through Series A startups.

Master the uv package manager for fast Python dependency management, virtual environments, and modern Python project workflows. Use when setting up Python projects, managing dependencies, or optimizing Python development workflows with uv.

Implement Command Query Responsibility Segregation for scalable architectures. Use when separating read and write models, optimizing query performance, or building event-sourced systems.

Implement data quality validation with Great Expectations, dbt tests, and data contracts. Use when building data quality pipelines, implementing validation rules, or establishing data contracts.

Expert SRE incident responder specializing in rapid problem resolution, modern observability, and comprehensive incident management. Masters incident command, blameless post-mortems, error budget management, and system reliability patterns. Handles critical outages, communication strategies, and continuous improvement. Use IMMEDIATELY for production incidents or SRE practices.

You are a monitoring and observability expert specializing in implementing comprehensive monitoring solutions. Set up metrics collection, distributed tracing, log aggregation, and create insightful da

This skill should be used when the user asks to "create financial projections", "build a financial model", "forecast revenue", "calculate burn rate", "estimate runway", "model cash flow", or requests 3-5 year financial planning for a startup.

Build production Apache Airflow DAGs with best practices for operators, sensors, testing, and deployment. Use when creating data pipelines, orchestrating workflows, or scheduling batch jobs.

Use this skill when working with Conductor's context-driven development methodology, managing project context artifacts, or understanding the relationship between product.md, tech-stack.md, and workflow.md files.

Migration monitoring, CDC, and observability infrastructure

Implement saga patterns for distributed transactions and cross-aggregate workflows. Use when coordinating multi-step business processes, handling compensating transactions, or managing long-running workflows.

Understand anti-reversing, obfuscation, and protection techniques encountered during software analysis. Use when analyzing protected binaries, bypassing anti-debugging for authorized analysis, or understanding software protection mechanisms.

Generate comprehensive C4 architecture documentation for an existing repository/codebase using a bottom-up analysis approach.

Automate changelog generation from commits, PRs, and releases following Keep a Changelog format. Use when setting up release workflows, generating release notes, or standardizing commit conventions.

Master Go concurrency with goroutines, channels, sync primitives, and context. Use when building concurrent Go applications, implementing worker pools, or debugging race conditions.

Master Julia 1.10+ with modern features, performance optimization, multiple dispatch, and production-ready practices. Expert in the Julia ecosystem including package management, scientific computing, and high-performance numerical code. Use PROACTIVELY for Julia development, optimization, or advanced Julia patterns.

Build production ML systems with PyTorch 2.x, TensorFlow, and modern ML frameworks. Implements model serving, feature engineering, A/B testing, and monitoring. Use PROACTIVELY for ML model deployment, inference optimization, or production ML infrastructure.

Master monorepo management with Turborepo, Nx, and pnpm workspaces to build efficient, scalable multi-package repositories with optimized builds and dependency management. Use when setting up monorepos, optimizing builds, or managing shared dependencies.

Master network protocol reverse engineering including packet analysis, protocol dissection, and custom protocol documentation. Use when analyzing network traffic, understanding proprietary protocols, or debugging network communication.

Generate comprehensive investor-ready business case document with market, solution, financials, and strategy

Expert C4 Code-level documentation specialist. Analyzes code directories to create comprehensive C4 code-level documentation including function signatures, arguments, dependencies, and code structure. Use when documenting code at the lowest C4 level for individual directories and code modules.

Master systematic debugging techniques, profiling tools, and root cause analysis to efficiently track down bugs across any codebase or technology stack. Use when investigating bugs, performance issues, or unexpected behavior.

You are a configuration management expert specializing in validating, testing, and ensuring the correctness of application configurations. Create comprehensive validation schemas, implement configurat

You are an **expert onboarding specialist and knowledge transfer architect** with deep experience in remote-first organizations, technical team integration, and accelerated learning methodologies. You

Professional, ethical HR partner for hiring, onboarding/offboarding, PTO and leave, performance, compliant policies, and employee relations. Ask for jurisdiction and company context before advising; produce structured, bias-mitigated, lawful templates.

Develop native iOS applications with Swift/SwiftUI. Masters iOS 18, SwiftUI, UIKit integration, Core Data, networking, and App Store optimization. Use PROACTIVELY for iOS-specific features, App Store optimization, or native iOS development.

Write and maintain Architecture Decision Records (ADRs) following best practices for technical decision documentation. Use when documenting significant technical decisions, reviewing past architectural choices, or establishing decision processes.

Optimize Apache Spark jobs with partitioning, caching, shuffle optimization, and memory tuning. Use when improving Spark performance, debugging slow jobs, or scaling data processing pipelines.

Initialize project with Conductor artifacts (product definition, tech stack, workflow, style guides)

Display project status, active tracks, and next actions

Execute tasks from a track's implementation plan following TDD workflow

Create a new track with specification and phased implementation plan

Build features guided by data insights, A/B testing, and continuous measurement using specialized agents for analysis, implementation, and experimentation.

Execute database migrations across ORMs and platforms with zero-downtime strategies, data transformation, and rollback procedures. Use when migrating databases, changing schemas, performing data transformations, or implementing zero-downtime deployment strategies.

Implement distributed tracing with Jaeger and Tempo to track requests across microservices and identify performance bottlenecks. Use when debugging microservices, analyzing request flows, or implementing observability for distributed systems.

Create structured incident response runbooks with step-by-step procedures, escalation paths, and recovery actions. Use when building runbooks, responding to incidents, or establishing incident response procedures.

Master memory forensics techniques including memory acquisition, process analysis, and artifact extraction using Volatility and related tools. Use when analyzing memory dumps, investigating incidents, or performing malware analysis from RAM captures.

Master Minecraft server plugin development with Bukkit, Spigot, and Paper APIs. Specializes in event-driven architecture, command systems, world manipulation, player management, and performance optimization. Use PROACTIVELY for plugin architecture, gameplay mechanics, server-side features, or cross-version compatibility.

Implement NFT standards (ERC-721, ERC-1155) with proper metadata handling, minting strategies, and marketplace integration. Use when creating NFT contracts, building NFT marketplaces, or implementing digital asset systems.

Master on-call shift handoffs with context transfer, escalation procedures, and documentation. Use when transitioning on-call responsibilities, documenting shift summaries, or improving on-call processes.

Implement comprehensive observability for service meshes including distributed tracing, metrics, and visualization. Use when setting up mesh monitoring, debugging latency issues, or implementing SLOs for service communication.

Master binary analysis patterns including disassembly, decompilation, control flow analysis, and code pattern recognition. Use when analyzing executables, understanding compiled code, or performing static analysis on binaries.

Orchestrate a comprehensive legacy system modernization using the strangler fig pattern, enabling gradual replacement of outdated components while maintaining continuous business operations through ex

Master advanced Git workflows including rebasing, cherry-picking, bisect, worktrees, and reflog to maintain clean history and recover from any situation. Use when managing complex Git histories, collaborating on feature branches, or troubleshooting repository issues.

Configure and optimize Nx monorepo workspaces. Use when setting up Nx, configuring project boundaries, optimizing build caching, or implementing affected commands.

Generate comprehensive market opportunity analysis with TAM/SAM/SOM calculations

Optimize Bazel builds for large-scale monorepos. Use when configuring Bazel, implementing remote execution, or optimizing build performance for enterprise codebases.

Manage major dependency version upgrades with compatibility analysis, staged rollout, and comprehensive testing. Use when upgrading framework versions, updating major dependencies, or managing breaking changes in libraries.

Master ShellCheck static analysis configuration and usage for shell script quality. Use when setting up linting infrastructure, fixing code issues, or ensuring script portability.

Define and implement Service Level Indicators (SLIs) and Service Level Objectives (SLOs) with error budgets and alerting. Use when establishing reliability targets, implementing SRE practices, or measuring service performance.

Write modern C# code with advanced features like records, pattern matching, and async/await. Optimizes .NET applications, implements enterprise patterns, and ensures comprehensive testing. Use PROACTIVELY for C# refactoring, performance optimization, or complex .NET solutions.

Use when working with full stack orchestration full stack feature

Create and manage production Grafana dashboards for real-time visualization of system and application metrics. Use when building monitoring dashboards, visualizing metrics, or creating operational observability interfaces.

Use when working with incident response incident response

Draft privacy policies, terms of service, disclaimers, and legal notices. Creates GDPR-compliant texts, cookie policies, and data processing agreements. Use PROACTIVELY for legal documentation, compliance texts, or regulatory requirements.

Configure mutual TLS (mTLS) for zero-trust service-to-service communication. Use when implementing zero-trust networking, certificate management, or securing internal service communication.

Expert web researcher using advanced search techniques and synthesis. Masters search operators, result filtering, and multi-source verification. Handles competitive analysis and fact-checking. Use PROACTIVELY for deep research, information gathering, or trend analysis.

Configure Turborepo for efficient monorepo builds with local and remote caching. Use when setting up Turborepo, optimizing build pipelines, or implementing distributed caching.

Write efficient C code with proper memory management, pointer arithmetic, and system calls. Handles embedded systems, kernel modules, and performance-critical code. Use PROACTIVELY for C optimization, memory issues, or system programming.