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Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).

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Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 and Bergquist 2025 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.

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AWS S3 object storage for bucket management, object operations, and access control. Use when creating buckets, uploading files, configuring lifecycle policies, setting up static websites, managing permissions, or implementing cross-region replication.

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Configure S3 buckets, policies, and lifecycle rules. Implement versioning, replication, and security. Use when managing object storage on AWS.

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Validate and stream file uploads securely with Validation and S3 streaming in NestJS. Use when implementing secure file uploads, validation, or S3 streaming in NestJS.

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Poisson-model peak caller for ChIP-seq/ATAC-seq BAMs. MACS3 callpeak finds enriched regions (TF sites or histone marks) vs input/IgG; outputs BED narrowPeak/broadPeak for motif analysis, annotation, and differential binding. Use narrow peaks for TF ChIP-seq and ATAC-seq; broad for H3K27me3, H3K9me3, and other broad marks.

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Configure S3 buckets, policies, and lifecycle rules. Implement versioning, replication, and security. Use when managing object storage on AWS.

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Add custom metadata headers (x-amz-meta-*) to AWS v4 signed requests for GCS S3-compatible API. Use when: (1) Adding custom metadata to GCS uploads via S3 API, (2) Getting signature mismatch errors after adding new headers, (3) x-amz-meta-* headers being ignored or causing 403 errors. Custom headers MUST be included in canonical headers and signed headers list.

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Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.

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Use Amazon Transcribe for AWS-based speech-to-text production: batch S3 transcription, real-time streaming, captions/subtitles, diarization, channel identification, custom vocabularies, vocabulary filters, language identification, PII/PHI handling, toxicity detection, Call Analytics, Medical, and secure S3/IAM/KMS workflows.

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The AWS Command Line Interface (v2) manages Amazon Web Services from the terminal. Use when the user needs to run S3, EC2, Lambda, CloudWatch, IAM or other AWS commands, sign in with SSO or short-term credentials, write AWS automation scripts, or debug an `aws` command and its output.

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Helper skill for using Hyperlane CLI address conversion utilities (addressToBytes32 and bytes32ToAddress) for cross-chain message formatting

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Expert guide for file uploads (S3, R2, Supabase Storage), presigned URLs, image/video processing, CDN optimization, and media pipeline architecture / Panduan ahli untuk upload file (S3, R2, Supabase Storage), presigned URL, pemrosesan gambar/video, optimasi CDN, dan arsitektur pipeline media.

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Use when the user wants to run SQL - especially analytical SQL - on local files (parquet/csv/json), URLs, S3 paths, or remote databases (Postgres, MySQL, MongoDB, ClickHouse Cloud, Iceberg, Delta Lake) without setting up a server. Provides chDB - embedded ClickHouse SQL in Python with 1000+ functions, Session for stateful multi-step pipelines, parametrized queries, and cross-source joins via `s3()`, `mysql()`, `postgresql()`, `iceberg()`, `deltaLake()`, `remoteSecure()` table functions. TRIGGER when: user wants SQL on parquet/csv/files or across remote analytical sources; uses ClickHouse SQL features (window functions, windowFunnel, geoToH3, JSON path ops, Session, parametrized queries); imports `chdb` or calls `chdb.query()`. SKIP this skill for pandas-style DataFrame method-chaining (use chdb-datastore instead) or ClickHouse server administration.

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Work with the @upstash/blob TypeScript/JavaScript SDK for S3-compatible object storage with direct browser uploads, presigned URLs, multipart, and signed reads. Use when storing files or blobs, uploading avatars, images, videos, attachments or user documents, letting a browser upload straight to storage without proxying bytes through a server, generating public or time-limited signed URLs, serving private files, streaming large files with pause and resume, setting cache headers on stored objects, or reaching an S3-compatible bucket from the AWS SDK.

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Penetration test AWS cloud environments for misconfigurations, privilege escalation, data exposure, and lateral movement. Use this skill when assessing AWS accounts for security weaknesses including S3 bucket misconfigurations, IAM policy flaws, EC2 metadata exploitation, Lambda function abuse, and cross-account attack paths. Covers both external and authenticated AWS pentesting.

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Use when configuring django-storages for cloud file storage - STORAGES setting, Amazon S3, Google Cloud Storage and Azure backends, signed URLs, CDN and caching, multipart uploads, or storage testing

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分布式并行策略选型与实测（USP / CP 通信掩盖 / CFG / TP/RSP/PP 概览；含拓扑相关选型 （按实测拓扑分域条件化：域内 bulk vs 跨域 head-parallel 翻转）与 AlltoAllV 缺陷绕过）。在 model-auto-optimization 中承担 S3：优先 USP、结合拓扑带宽差异选 CP，少量 step + 多 rank 验证特性开启与掩盖（产物：并行方案 + 多 rank 证据）。当用户需要多卡并行 策略选择、**序列并行形态抉择**（纯 Ulysses vs 复合 AllGather-KV×Ulysses：按 GQA / 跨域带宽 / 形态 plumbing 条件化定胜负）、**并行 × 稀疏叠加**（seam 契约：先汇聚后稀疏、 窗口偏移、块对齐、per-head 掩码；含「稀疏看似生效实则未生效」判定）、通信掩盖调优 （含**掩盖率上限**：1-1/n 何时成立、c/f 决定的真实上限、没生效的排查）、**并行方案 差异归因**（阶段 Δ 分解 / 集合通信按 communicator 归属 / 4→8 卡线性度），或排查多卡 跑不动 / 通信暴露大 / 换卡组 / 端口 bind / HCCL 带宽验证问题时使用；**并收编原并行作用域诊断**： 改了 SP/CP/Ulysses/AllGather-KV 后**不报错但结果没变/性能没变**、或小规模能跑大规模崩 （如 Ascend EE1003 coreDim 超限）时，用本技能证明"改动到底有没有生效"（判别量逐层收窄 + 两侧对照 + 日志≠生效，见 `references/scope-effectiveness-check.md`）； 即使用户只说 "多卡跑不动""通信暴露大""为什么没达到 6/7 的掩盖率""CP 和 USP 该选哪个""CP 叠稀疏 怎么不生效"而未说并行，也应触发。特性档位/接口事实见 `docs/zh/features/parallelism.md` /`usp.md`（仓内真源），框架侧开启见 framework-integration； 本技能承载选型决策、monkey-patch 掩盖与多卡诊断实测。 由 dev-workflow 多卡场景触发，亦由 model-auto-optimization 的 S3 阶段触发。

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Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM), MeTPeak (HMM over sliding windows), MACS3/MACS2 with --nomodel --broad --keep-dup all (genome-wide broad alternative), and DRACH motif enrichment via HOMER or ggseqlogo as a sanity check (NOT a filter). Covers BED12 vs narrowPeak output, exonic vs intronic peak handling, multi-tool reconciliation (intersection vs union), the m6A-vs-m6Am ambiguity at 5'UTR peaks that antibody methods cannot resolve, and orthogonal validation (miCLIP/GLORI/m6A-SAC-seq/m6Anet). Use when calling peaks from paired IP/input genome BAMs, choosing exomePeak2 (transcript-aware default) vs MACS3 (broad genomic) vs MeTPeak (HMM-smoothed low-coverage), confirming DRACH enrichment as a sanity check on the peak set, reconciling differing peak sets across tools, validating MeRIP peaks against single-base methods, interpreting 5' peaks where m6Am contamination is possible, or recommending a consensus strategy.

日本語の概要は準備中です。原文の説明を表示しています。

Processes eDNA metabarcoding from raw paired-end reads to species tables, navigating ASV (DADA2, UNOISE3) vs OTU (swarm v2) decision (Callahan 2017 vs Schloss multi-copy-16S critique), marker/primer choice (Leray COI, MiFish 12S, 515F/806R 16S, ITS2) with primer-specific bias, OBITools3 v3 command-name break (obi stats plural; .tar.gz taxonomy), tag-jumping with dual-indexing (Schnell 2015; NovaSeq 10x MiSeq), decontam as screening-not-classifier (Davis 2018), read-counts-not-abundance critique (Lamb 2019), site-occupancy modeling (Ficetola 2015), Naive-Bayes calibration limits (Bokulich 2018), and eDNA decay (Strickler 2015). Use when going from raw eDNA FASTQ to species tables, picking marker + denoising pipeline, deciding whether read counts represent abundance, applying occupancy modeling, configuring OBITools3 v3, or interpreting decontam output. Not for clinical 16S microbiome (see microbiome/amplicon-processing).

日本語の概要は準備中です。原文の説明を表示しています。

Applies ACMG/AMP 2015 framework with ClinGen SVI specifications, Tavtigian 2018/2020 Bayesian point system, Abou Tayoun 2018 PVS1 decision tree, Pejaver 2022 and Bergquist 2025 calibrated PP3/BP4 thresholds for REVEL/BayesDel/AlphaMissense, Brnich 2020 PS3/BS3 OddsPath, Walker 2023 SpliceAI splicing framework, and AMP/ASCO/CAP 2017 tumor tiers. Use when classifying germline variants P / LP / VUS / LB / B, applying VCEP-specific CSpec rules, computing Whiffin BS1, or assigning cancer Tier I-IV per Li 2017.

日本語の概要は準備中です。原文の説明を表示しています。

Use when running analytical SQL over Parquet/CSV/JSON without a warehouse, replacing pandas for data wrangling, joining S3 data in-place, building local data marts, or embedding OLAP into an app. Triggers: read_parquet/read_csv setup, partitioned dataset queries, hive partitioning, glob patterns for S3, COPY TO export, attach Postgres/MySQL, UDFs in Python/R, MotherDuck cloud sync, columnar performance vs row stores. NOT for OLTP workloads (concurrent writes), distributed analytics at petabyte scale (use Spark/Trino), or vector search (use pgvector/Lance).

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Detect abnormal access patterns in AWS S3, GCS, and Azure Blob Storage by analyzing CloudTrail Data Events, GCS audit logs, and Azure Storage Analytics. Identifies after-hours bulk downloads, access from new IP addresses, unusual API calls (GetObject spikes), and potential data exfiltration using statistical baselines and time-series anomaly detection.

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AWS CLIの専門家スキル。EC2, S3, IAM, Lambda, RDS, ECS等の主要サービスのCLI操作を支援。IAMポリシー設計、クロスアカウント運用、セキュリティ設定、コスト最適化のベストプラクティスを提供。Use when working with AWS services via CLI, designing IAM policies, managing infrastructure, or automating cloud operations.