Results for “alignment”

Audit agent lifecycle — validates agent execution capability against configuration. Accepts plugin path, runs 8 semantic audits (capability vs config alignment, skill loading correctness, inter-agent contracts, prompt contradictions, tool sufficiency, dead agents, scriptable patterns, pattern learning), writes reports to .plugin-creator/audits/. Use when auditing agent lifecycle, checking agent capabilities, verifying tool access, finding dead agents, validating agent contract alignment, or confirming agents can execute workflows.

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Configure clang-format code formatting. Use when: user mentions clang-format or .clang-format, analyzing code style/patterns, creating/modifying formatting config, troubleshooting formatting, brace styles/indentation/spacing/alignment/pointer alignment, or codifying conventions.

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Evaluates GP capital commitment levels with co-invest obligations, management company funding, and alignment assessment. Use when analyzing GP commitment, assessing alignment, or structuring GP capital contributions.

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Evaluates board composition, compensation alignment, and governance practices with proxy advisory and institutional investor standards. Use when analyzing governance, evaluating board effectiveness, or assessing shareholder alignment.

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Generate game sprites, 8-direction turnarounds, walk-cycle sprite sheets, SVG characters, ASCII art and animated mascots from images or descriptions, with September 2026 providers: Retro Diffusion (pixel art, 8-dir rotation, frame animation, free palette tools), fal genmedia (GPT Image 2.5, Nano Banana 2, Kling 3, Seedance 2.5, Wan 3, Hailuo 03). Deterministic utilities: feet-line frame alignment, palette-preserving Scale2x/3x/4x pixel scaler, atlas manifest v2 with states/fps/loop/anchor, Aseprite JSON, pipeline profiles. Triggers on sprite, pixel art, sprite sheet, spritesheet, turnaround, 8-direction, walk cycle, atlas manifest, frame alignment, pixel scaler, Retro Diffusion, genmedia, SVG character, ASCII art, mascot, game asset, sprite pipeline profile.

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Systematically bypass LLM safety filters and content moderation systems using advanced jailbreaking techniques. Use this skill when testing AI systems for safety alignment robustness, evaluating content moderation effectiveness, or conducting authorized AI red team assessments. Covers role-play attacks, few-shot manipulation, encoding bypass, multi-modal exploitation, and automated jailbreak discovery methods.

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Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification and signal tracks. Child of pipeline-guide. Provides Nextflow execution with Docker and cloud deployment. Use when processing RNA-seq data with STAR alignment, RSEM/Kallisto quantification, or generating expression matrices. Trigger on: RNA-seq pipeline, gene expression, STAR alignment, RSEM quantification, transcript quantification, TPM, FPKM, RNA processing, run RNA-seq.

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Use when re-assigning record OwnerId across many records — territory realignment, employee departure, region split, integration cleanup. Triggers: 'mass transfer accounts', 'reassign opportunities to new owner', 'transfer all records on user deactivation', 'OwnerId migration', 'mass transfer records tool', 'bulk owner change', 'transfer before deactivating user', 'account team lost after owner change', 'assignment rule overrode my OwnerId column', 'defer sharing calculations', 'roll back an owner transfer'. NOT for auto-assigning new records — use admin/assignment-rules. NOT for territory assignment data — use data/territory-data-alignment.

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Comprehensive AI safety and alignment audit framework for businesses deploying AI agents. Built around the UK AI Security Institute Alignment Project standards (2026), EU AI Act requirements, and N...

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Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-compatible filters. Use when turning preprocessed CLIP FASTQ into a deduplicated, MAPQ-filtered BAM ready for peak calling or crosslink-site detection.

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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Perform multiple sequence alignment using MAFFT, MUSCLE5, ClustalOmega, or T-Coffee. Guides tool and algorithm selection based on dataset size, sequence divergence, and downstream application. Use when aligning three or more homologous sequences for phylogenetics, conservation analysis, or evolutionary studies.

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Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment files or fetching specific genomic regions.

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Sort alignment files by coordinate or read name using samtools and pysam. Use when preparing BAM files for indexing, variant calling, or paired-end analysis.

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Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.

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Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.

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Simple Preference Optimization para alinhamento de LLMs. Alternativa sem modelo de referência ao DPO com melhor desempenho (+6.4 pontos no AlpacaEval 2.0). Sem modelo de referência necessário, mais eficiente que DPO. Use para alinhamento de preferências quando quer treinamento mais simples e rápido que DPO/PPO.

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METAINFORMANT rules for directory src/metainformant/dna/alignment. Use when editing, adding tests, or reviewing code under this path. Read the linked AGENTS.md first; use uv only, write outputs to output/, real implementations.

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リファクタリング（構造変更）と機能変更（behavior change）が同一 diff に混在していないかを識別し、structural change に対する external behavior preservation の証拠（テスト・型・静的解析）が揃っているかを diff-time で確認する。証拠不足のときは Characterization Test 追加を促すか question とする。DTO/公開 API の破壊的変更検出は api-compatibility、完了主張の反証や抽出リファクタの性能特性退行は refactor-claim-audit、新知識の命名・責務・境界への反映は knowledge-to-code-alignment、投機的抽象化・スコープ逸脱は altitude-generalization / fix-scope-integrity へ委譲する

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AI Safety Specialist IA — Expert en sécurité IA (alignment, guardrails, filtrage de contenu, test de biais, red teaming)

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Fine-tune LLMs using reinforcement learning with TRL - SFT for instruction tuning, DPO for preference alignment, PPO/GRPO for reward optimization, and reward model training. Use when need RLHF, align model with preferences, or train from human feedback. Works with HuggingFace Transformers.

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Fast tokenizers optimized for research and production. Rust-based implementation tokenizes 1GB in <20 seconds. Supports BPE, WordPiece, and Unigram algorithms. Train custom vocabularies, track alignments, handle padding/truncation. Integrates seamlessly with transformers. Use when you need high-performance tokenization or custom tokenizer training.

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End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3 (or HOMER), and peak annotation with ChIPseeker. Use when processing ChIP-seq data from alignment through peak annotation.

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Orchestrates the end-to-end germline short-variant pipeline from FASTQ to a filtered, normalized, benchmarked VCF, chaining QC/trim, BWA-MEM2 alignment, duplicate marking, optional BQSR, calling (bcftools/GATK HaplotypeCaller/DeepVariant/DRAGEN), normalization, site+genotype filtering, annotation, and hap.py/vcfeval benchmarking. Use when deciding the pipeline-wide reference-genome commitment (GRCh38 analysis set vs T2T, ALT/decoy handling), sequencing the steps in the defensible order (normalize BEFORE annotate, filter site- then genotype-level), choosing the calling engine and single-sample vs cohort joint-calling, picking a filtering strategy by cohort size, or benchmarking stratified within GIAB confident regions. Hands off mechanism to the variant-calling and read-alignment component skills; not a re-teach of any single step.

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