“assembly”的搜索结果

Assembles haplotype-resolved diploid and telomere-to-telomere (T2T) genomes from PacBio HiFi reads with hifiasm (HiFi-only, Hi-C, or trio phasing) and verkko (HiFi + ultralong ONT for T2T), extracting contigs from GFA and routing phasing QC to k-mer/trio metrics. Covers why a primary assembly is a haplotype mosaic that exists in no cell, partial-vs-full phasing (the .bp. vs .dip. filename convention), the purge-default trap on inbred samples, the --hom-cov coverage-estimate alarm, and verkko-vs-hifiasm for T2T. Use when assembling a diploid eukaryote from HiFi, phasing haplotypes with parents (trio) or Hi-C, deciding whether to chase T2T, or diagnosing switch errors invisible to N50/BUSCO/QV.

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AssemblyAI integration. Manage Transcripts, Speakers, Jobs. Use when the user wants to interact with AssemblyAI data.

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Workflow for de novo assembly, scaffolding, polishing, contamination review, and assembly QC.

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AssemblyAI is a hosted speech-to-text API that transcribes audio and video files or live streams and adds speaker labels, sentiment, entity detection, PII redaction and LLM analysis of the transcript. Use when a user asks to transcribe a recording, label who said what, analyze call sentiment, redact personal data, stream live transcription, or summarize and question a transcript with LLM Gateway (the replacement for LeMUR).

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Expert in Ethereum Virtual Machine internals - gas optimization, assembly/Yul, opcode-level optimization, and low-level EVM patternsUse when "evm, gas optimization, yul, inline assembly, opcodes, solidity optimization, evm bytecode, storage layout, evm, ethereum, solidity, yul, assembly, gas-optimization, opcodes, smart-contracts" mentioned.

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语音转文字 (ASR) (语音转文字 (ASR / 语音识别 / Speech-to-Text) 应用工程 (从业者视角) — 选型、集成、优化语音转文字能力，尤其面向移动端、低成本、快速识别的场景。覆盖: (a) 引擎/API 地图 — 云端 API(OpenAI gpt-4o-transcribe / Whisper API、Deepgram、AssemblyAI、Google / Azure / AWS Transcribe、讯飞、字节火山、阿里、腾讯、百度) vs 开源模型(Whisper / faster-whisper / whisper.cpp / distil-whisper、NVIDIA NeMo Parakeet / Canary、阿里 FunASR / Paraformer / SenseVoice、Moonshine、Vosk、Kaldi / k2 / icefall) vs 端侧·移动 SDK(whisper.cpp + CoreML / Metal、iOS Speech framework、Android SpeechRecognizer、Picovoice、SenseVoice 端侧); (b) 准确率(WER / CER) × 延迟(RTF / 流式) × 成本 三角权衡与选型决策树; (c) 成本优化 playbook — 端侧免费 / 批量折扣 / VAD 裁静音 / 量化(int8 / ggml) / 蒸馏 / 自托管 break-even; (d) 移动端集成 — 端侧 vs 云、流式 vs 批量、断点检测(endpointing)、隐私 / 离线; (e) 后处理 — 标点 / 数字规整(ITN) / 说话人分离(diarization) / 时间戳。学派分歧: 云 API vs 端侧自托管、通用大模型(Whisper) vs 专用流式(RNN-T / Conformer)、闭源 API vs 开源、准确率派 vs 成本派、英文优先 vs 中文 ASR(FunASR / SenseVoice / 讯飞)。不含: 文字转语音(TTS / 语音合成，方向相反)、声纹识别 / 说话人验证为主业、语音 agent / 对话式 AI、ASR 模型训练科研深水区。) Master OS — automated mastery of 语音转文字 (ASR / 语音识别 / Speech-to-Text) 应用工程 (从业者视角) — 选型、集成、优化语音转文字能力，尤其面向移动端、低成本、快速识别的场景。覆盖: (a) 引擎/API 地图 — 云端 API(OpenAI gpt-4o-transcribe / Whisper API、Deepgram、AssemblyAI、Google / Azure / AWS Transcribe、讯飞、字节火山、阿里、腾讯、百度) vs 开源模型(Whisper / faster-whisper / whisper.cpp / distil-whisper、NVIDIA NeMo Parakeet / Canary、阿里 FunASR / Paraformer / SenseVoice、Moonshine、Vosk、Kaldi / k2 / icefall) vs 端侧·移动 SDK(whisper.cpp + CoreML / Metal、iOS Speech framework、Android SpeechRecognizer、Picovoice、SenseVoice 端侧); (b) 准确率(WER / CER) × 延迟(RTF / 流式) × 成本 三角权衡与选型决策树; (c) 成本优化 playbook — 端侧免费 / 批量折扣 / VAD 裁静音 / 量化(int8 / ggml) / 蒸馏 / 自托管 break-even; (d) 移动端集成 — 端侧 vs 云、流式 vs 批量、断点检测(endpointing)、隐私 / 离线; (e) 后处理 — 标点 / 数字规整(ITN) / 说话人分离(diarization) / 时间戳。学派分歧: 云 API vs 端侧自托管、通用大模型(Whisper) vs 专用流式(RNN-T / Conformer)、闭源 API vs 开源、准确率派 vs 成本派、英文优先 vs 中文 ASR(FunASR / SenseVoice / 讯飞)。不含: 文字转语音(TTS / 语音合成，方向相反)、声纹识别 / 说话人验证为主业、语音 agent / 对话式 AI、ASR 模型训练科研深水区。: top builders' mental models, tool stack, current workflows, jargon, and where to keep up. Trigger this skill when the user works on 语音转文字 (ASR / 语音识别 / Speech-to-Text) 应用工程 (从业者视角) — 选型、集成、优化语音转文字能力，尤其面向移动端、低成本、快速识别的场景。覆盖: (a) 引擎/API 地图 — 云端 API(OpenAI gpt-4o-transcribe / Whisper API、Deepgram、AssemblyAI、Google / Azure / AWS Transcribe、讯飞、字节火山、阿里、腾讯、百度) vs 开源模型(Whisper / faster-whisper / whisper.cpp / distil-whisper、NVIDIA NeMo Parakeet / Canary、阿里 FunASR / Paraformer / SenseVoice、Moonshine、Vosk、Kaldi / k2 / icefall) vs 端侧·移动 SDK(whisper.cpp + CoreML / Metal、iOS Speech framework、Android SpeechRecognizer、Picovoice、SenseVoice 端侧); (b) 准确率(WER / CER) × 延迟(RTF / 流式) × 成本 三角权衡与选型决策树; (c) 成本优化 playbook — 端侧免费 / 批量折扣 / VAD 裁静音 / 量化(int8 / ggml) / 蒸馏 / 自托管 break-even; (d) 移动端集成 — 端侧 vs 云、流式 vs 批量、断点检测(endpointing)、隐私 / 离线; (e) 后处理 — 标点 / 数字规整(ITN) / 说话人分离(diarization) / 时间戳。学派分歧: 云 API vs 端侧自托管、通用大模型(Whisper) vs 专用流式(RNN-T / Conformer)、闭源 API vs 开源、准确率派 vs 成本派、英文优先 vs 中文 ASR(FunASR / SenseVoice / 讯飞)。不含: 文字转语音(TTS / 语音合成，方向相反)、声纹识别 / 说话人验证为主业、语音 agent / 对话式 AI、ASR 模型训练科研深水区。 problems and wants industry-grade thinking, tool selection, or workflow guidance. 触发词：「语音转文字」「语音识别」「asr」「speech to text」「stt」

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Lee Cronin's Assembly Theory for molecular complexity measurement and life detection via assembly index computation.

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Transcribes audio and generates auto-chapters with summaries using AssemblyAI's /v2/transcript endpoint with auto_chapters=true. Extracts key topics, sentiment analysis, and content safety labels via AssemblyAI SDK.

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Streams audio from Twilio Media Streams over WebSocket to AssemblyAI real-time transcription, extracting speaker-diarized transcripts with word-level timestamps. Triggers entity detection and sentiment analysis via AssemblyAI LeMUR on completed call segments. Results are pushed to HubSpot or Salesforce contact records via their REST APIs.

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Extract structured intelligence from audio using the AssemblyAI API with sentiment analysis, entity detection, topic modeling, and auto-chapter generation. Uses the assemblyai Python SDK for transcript processing pipelines.

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Three-tier video pipeline: ffmpeg Quick (5s, instant) → ffmpeg Enhanced with Ken Burns (15s, polished) → Remotion Animated (60-90s, production-grade). Takes static slides from Paper MCP or any PNGs and assembles them into platform-ready video. Make sure to use this skill whenever the user has slides, images, or PNGs and wants to turn them into video — even if they just say 'make a video from these', 'animate my slides', 'I have images and need a TikTok', or 'stitch these together'. Also use when they mention ffmpeg video assembly, Remotion-animated slide assembly, Ken Burns effects, or any slides-to-video pipeline. Owns the slides→MP4 assembly pipeline; for writing, debugging, or running `remotion render` on Remotion code itself, see /remotion-best-practices; for screen-recorded product demos, see /marketing-demo. Works with any PNG source — Paper exports, Canva, screenshots, anything.

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Reverse engineers malware binaries using NSA's Ghidra disassembler and decompiler to understand internal logic, cryptographic routines, C2 protocols, and evasion techniques at the assembly and pseudo-C level. Activates for requests involving malware reverse engineering, disassembly analysis, decompilation, binary analysis, or understanding malware internals.

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End-to-end shotgun metagenomics workflow from FASTQ to taxonomic and functional profiles, orchestrating controls/host depletion, Kraken2+Bracken classification, MetaPhlAn marker profiling, and HUMAnN functional profiling. Covers the controls-first ordering, why Kraken2 read counts are not abundances and MetaPhlAn cell fractions do not equal Bracken read fractions, and the consistent-pipeline framing. Use when profiling shotgun metagenomic samples end to end, or chaining classification, abundance, and function. For resistome see metagenomics/amr-detection; for strains see metagenomics/strain-tracking; for assembly see genome-assembly/metagenome-assembly.

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Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT (low-memory, huge datasets), Unicycler (bacterial finishing/hybrid), MaSuRCA (large hybrid), ABySS (Bloom-filter), and Platanus (heterozygous diploids), using multi-k de Bruijn graphs. Covers the repeat-resolution limit, why N50 plateaus at the genome not the depth, GenomeScope2 k-mer profiling first, the heterozygosity/haplotig trap, error-correction erasing rare alleles, GC dropout, and NG50/auN/BUSCO reporting. Use when assembling a bacterial isolate, fungal, small-eukaryotic, single-cell, or metagenome genome from Illumina reads, or when deciding whether short reads can even produce the assembly being asked for.

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Assembles microbial-community sequencing into metagenome-assembled genomes (MAGs) with metaFlye (ONT), metaSPAdes/MEGAHIT (Illumina), and hifiasm-meta/metaMDBG (PacBio HiFi), then recovers genomes via multi-binner consolidation (MetaBAT2, MaxBin2, CONCOCT, SemiBin2, VAMB -> DAS_Tool) and QCs them against MIMAG with CheckM2, GUNC, and GTDB-Tk. Covers why a metagenome is not a genome (uneven coverage, micro-diversity, strain collapse to consensus), differential-coverage binning, co-assembly vs per-sample, the rRNA-operon collapse that fails short-read MAGs, and strain resolution with inStrain. Use when reconstructing genomes from a microbiome, soil, ocean, or gut community, recovering MAGs, or resolving strain-level variation.

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Detects and removes contamination in genome assemblies via two disjoint workflows - foreign-sequence screening of a single-organism (eukaryote/isolate) assembly with NCBI FCS-GX (GenBank-submission-mandatory), FCS-adaptor, and BlobToolKit blob plots; and MAG/bin quality assessment with CheckM2 plus GUNC (chimerism) plus GTDB-Tk taxonomy, judged against MIMAG. Covers why CheckM2 alone is blind to disjoint-marker chimeras, the FCS-GX RAM wall, organelle/NUMT triage, strain heterogeneity, and the HGT-vs-contamination (tardigrade) trap. Use when screening an assembly for foreign contamination before GenBank submission, assessing MAG completeness/contamination/chimerism, deciding which contigs to remove, or distinguishing real HGT from contaminant contigs.

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Assembles haplotype-resolved diploid and telomere-to-telomere (T2T) genomes from PacBio HiFi reads with hifiasm (HiFi-only, Hi-C, or trio phasing) and verkko (HiFi + ultralong ONT for T2T), extracting contigs from GFA and routing phasing QC to k-mer/trio metrics. Covers why a primary assembly is a haplotype mosaic that exists in no cell, partial-vs-full phasing (the .bp. vs .dip. filename convention), the purge-default trap on inbred samples, the --hom-cov coverage-estimate alarm, and verkko-vs-hifiasm for T2T. Use when assembling a diploid eukaryote from HiFi, phasing haplotypes with parents (trio) or Hi-C, deciding whether to chase T2T, or diagnosing switch errors invisible to N50/BUSCO/QV.

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Select, document, download, and checksum-verify the most appropriate NCBI reference genome on an HPC cluster. Use whenever an analysis needs a reference genome, genome FASTA, genome annotation, assembly accession, or genome index and no exact approved assembly is already available; when a user asks to fetch a species genome from NCBI; or when a pipeline must resolve and cache a reproducible reference assembly on a remote cluster.

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Detects and removes contamination in genome assemblies via two disjoint workflows - foreign-sequence screening of a single-organism (eukaryote/isolate) assembly with NCBI FCS-GX (GenBank-submission-mandatory), FCS-adaptor, and BlobToolKit blob plots; and MAG/bin quality assessment with CheckM2 plus GUNC (chimerism) plus GTDB-Tk taxonomy, judged against MIMAG. Covers why CheckM2 alone is blind to disjoint-marker chimeras, the FCS-GX RAM wall, organelle/NUMT triage, strain heterogeneity, and the HGT-vs-contamination (tardigrade) trap. Use when screening an assembly for foreign contamination before GenBank submission, assessing MAG completeness/contamination/chimerism, deciding which contigs to remove, or distinguishing real HGT from contaminant contigs.

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Assembles haplotype-resolved diploid and telomere-to-telomere (T2T) genomes from PacBio HiFi reads with hifiasm (HiFi-only, Hi-C, or trio phasing) and verkko (HiFi + ultralong ONT for T2T), extracting contigs from GFA and routing phasing QC to k-mer/trio metrics. Covers why a primary assembly is a haplotype mosaic that exists in no cell, partial-vs-full phasing (the .bp. vs .dip. filename convention), the purge-default trap on inbred samples, the --hom-cov coverage-estimate alarm, and verkko-vs-hifiasm for T2T. Use when assembling a diploid eukaryote from HiFi, phasing haplotypes with parents (trio) or Hi-C, deciding whether to chase T2T, or diagnosing switch errors invisible to N50/BUSCO/QV.

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Assembles microbial-community sequencing into metagenome-assembled genomes (MAGs) with metaFlye (ONT), metaSPAdes/MEGAHIT (Illumina), and hifiasm-meta/metaMDBG (PacBio HiFi), then recovers genomes via multi-binner consolidation (MetaBAT2, MaxBin2, CONCOCT, SemiBin2, VAMB -> DAS_Tool) and QCs them against MIMAG with CheckM2, GUNC, and GTDB-Tk. Covers why a metagenome is not a genome (uneven coverage, micro-diversity, strain collapse to consensus), differential-coverage binning, co-assembly vs per-sample, the rRNA-operon collapse that fails short-read MAGs, and strain resolution with inStrain. Use when reconstructing genomes from a microbiome, soil, ocean, or gut community, recovering MAGs, or resolving strain-level variation.

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Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT (low-memory, huge datasets), Unicycler (bacterial finishing/hybrid), MaSuRCA (large hybrid), ABySS (Bloom-filter), and Platanus (heterozygous diploids), using multi-k de Bruijn graphs. Covers the repeat-resolution limit, why N50 plateaus at the genome not the depth, GenomeScope2 k-mer profiling first, the heterozygosity/haplotig trap, error-correction erasing rare alleles, GC dropout, and NG50/auN/BUSCO reporting. Use when assembling a bacterial isolate, fungal, small-eukaryotic, single-cell, or metagenome genome from Illumina reads, or when deciding whether short reads can even produce the assembly being asked for.

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Select, document, download, and checksum-verify the most appropriate NCBI reference genome on an HPC cluster. Use whenever an analysis needs a reference genome, genome FASTA, genome annotation, assembly accession, or genome index and no exact approved assembly is already available; when a user asks to fetch a species genome from NCBI; or when a pipeline must resolve and cache a reproducible reference assembly on a remote cluster.

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Convert genomic positions between file conventions, standardize variant representations, and check reference genome or chromosome naming conflicts. The skill helps investigate one-base shifts and compare individual variants against a reference sequence before combining analysis files.

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• Converting coordinates between BED and GFF/GTF
• Standardizing and comparing insertion or deletion records
• Checking reference genome and chromosome naming conflicts