Results for “assembly”

Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm, and reconciles bacterial assemblies into a consensus with Trycycler/Autocycler. Covers matching the input flag to the basecaller era (--nano-hq vs --nano-raw), why a raw long-read assembly is contiguous but low-QV and not finished until polished, haplotig false-duplication and purge_dups, coverage and read-N50 as non-substitutable inputs, and mid-read adapter de-chimerization. Use when assembling a bacterial or eukaryotic genome from ONT or PacBio noisy reads, choosing a long-read assembler, or diagnosing an over-collapsed or duplicated assembly. For PacBio HiFi use hifi-assembly instead.

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Decides whether and how to polish a draft genome assembly to raise consensus accuracy (QV) with read-type-matched tools - Racon and medaka (ONT consensus), dorado polish, Polypolish and pypolca (Illumina, repeat-aware), Pilon (legacy short-read), NextPolish/NextPolish2, Hapo-G (haplotype-aware), ntEdit, and DeepPolisher/PEPPER-Margin-DeepVariant for human. Covers the do-not-polish-HiFi rule, the medaka basecaller-model footgun, held-out Merqury QV as the only honest stop signal, and the haplotype-collapse trap. Use when correcting homopolymer indels or residual SNPs in a long-read assembly, deciding if a HiFi assembly needs polishing, or choosing an ONT vs hybrid vs short-read polishing chain.

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Assembles genomes de novo from noisy long reads (Oxford Nanopore R9/R10/Dorado, PacBio CLR) with Flye (repeat graph), Canu (correct-trim-assemble OLC), NextDenovo, Shasta, Raven, wtdbg2, or miniasm, and reconciles bacterial assemblies into a consensus with Trycycler/Autocycler. Covers matching the input flag to the basecaller era (--nano-hq vs --nano-raw), why a raw long-read assembly is contiguous but low-QV and not finished until polished, haplotig false-duplication and purge_dups, coverage and read-N50 as non-substitutable inputs, and mid-read adapter de-chimerization. Use when assembling a bacterial or eukaryotic genome from ONT or PacBio noisy reads, choosing a long-read assembler, or diagnosing an over-collapsed or duplicated assembly. For PacBio HiFi use hifi-assembly instead.

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Integrate RuView through shell commands, an HTTP API, or WebAssembly builds, which run compiled code in browsers and supported edge devices. Covers survivor scan commands, result exports, API hosting, and browser or ESP32 deployment paths.

• Script survivor scans and export results
• Expose RuView sensing through HTTP
• Build RuView for browser use

Create and manage agents in WebAssembly, an execution environment that keeps their work isolated. Try untrusted code or agent configurations, manage sandbox files and tool access, and export agents for sharing.

• Trying untrusted code in an isolated environment
• Experimenting with agent configurations
• Reading and writing files inside an agent sandbox

Create a new ASP.NET Core web app with Blazor. Choose where pages and interactive components run based on application needs, generate the project with appropriate options, configure initial authentication when needed, and verify building and startup.

• Start a new Blazor website or web application
• Choose a rendering mode for the required interactivity
• Generate a project with individual account authentication

Organize gh-aw Go code with guidance on splitting files by function, placing shared helpers, and keeping tests near implementations. It also explains string cleanup conventions and replacement implementations for features unavailable in WebAssembly builds.

• Splitting large Go files by responsibility
• Choosing where to place shared helper functions
• Distinguishing character cleanup from format normalization

Analyze and triage AssemblyAI REST, transcript, Streaming v3, webhook, and LLM Gateway failures without leaking customer content. Use when an integration errors or stalls. Trigger with "AssemblyAI error" or "failed transcript".

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Build AssemblyAI CI with offline REST, Streaming v3, webhook, gateway, secret, and lifecycle tests plus a tightly gated live lane. Use when adding automated verification. Trigger with "AssemblyAI CI" or "contract test".

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Produce a redacted AssemblyAI diagnostic bundle for support and incident triage. Use when evidence is needed without exposing keys, URLs, audio, transcripts, or prompts. Trigger with "AssemblyAI debug bundle" or "support evidence".

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Analyze and operate a production AssemblyAI pre-recorded pipeline with explicit models, Speech Understanding, callbacks, and retention controls. Use when running asynchronous transcription. Trigger with "AssemblyAI async transcription" or "pre-recorded pipeline".

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Migrate legacy AssemblyAI Streaming v2 and LeMUR integrations to Streaming v3 and LLM Gateway with parity evidence. Use when removing deprecated contracts. Trigger with "migrate AssemblyAI", "LeMUR migration", or "Streaming v3 upgrade".

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Analyze and gate an AssemblyAI integration across contracts, security, reliability, cost, observability, retention, and rollback. Use when preparing a launch or material change. Trigger with "AssemblyAI production checklist" or "go live".

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PCBWay PCB fabrication and assembly — turnkey/consigned assembly, design rules, ordering workflow. Alternative to JLCPCB for manufacturing. Use with KiCad. Use this skill when the user mentions PCBWay, needs turnkey assembly (PCBWay sources parts by MPN), has parts not available on LCSC, needs assembled boards with non-LCSC components, wants to compare PCBWay vs JLCPCB, or needs assembly with parts sourced globally rather than from LCSC only. For gerber/CPL export, stencil ordering, and BOM management, see the `bom` skill.

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PCBWay PCB fabrication and assembly — turnkey/consigned assembly, design rules, ordering workflow. Alternative to JLCPCB for manufacturing. Use with KiCad. Use this skill when the user mentions PCBWay, needs turnkey assembly (PCBWay sources parts by MPN), has parts not available on LCSC, needs assembled boards with non-LCSC components, wants to compare PCBWay vs JLCPCB, or needs assembly with parts sourced globally rather than from LCSC only. For gerber/CPL export, stencil ordering, and BOM management, see the `bom` skill.

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Profiles a genome from raw reads BEFORE assembly with a k-mer spectrum (KMC or Jellyfish histogram), then models it with GenomeScope2 to estimate genome size, heterozygosity, repeat content, and ploidy, and Smudgeplot to infer ploidy from heterozygous k-mer pairs (diploid AB vs triploid AAB vs tetraploid AABB). Covers choosing k via Merqury best_k.sh, the k-mer-coverage vs sequencing-coverage confusion, reading het/repeat/contamination/organelle peaks, why noisy ONT must not be used for counting, and how the estimate becomes the NG50 denominator, the Flye -g value, the hifiasm --hom-cov/purge setting, and the 1.5-2x-too-big haplotig sanity check. Use when starting any de novo assembly, deciding whether short reads can work, estimating genome size for an unknown organism, diagnosing ploidy, or sanity-checking an assembly's size against expectation.

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Binary analysis, assembly interpretation, disassembly, decompilation, firmware RE, and protocol reverse engineering

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Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka). Essential for improving long-read assembly accuracy. Use when improving assembly accuracy with polishing tools.

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PCBWay PCB fabrication and assembly — turnkey/consigned assembly, design rules, ordering workflow. Alternative to JLCPCB for manufacturing. Use with KiCad. Use this skill when the user mentions PCBWay, needs turnkey assembly (PCBWay sources parts by MPN), has parts not available on LCSC, needs assembled boards with non-LCSC components, wants to compare PCBWay vs JLCPCB, or needs assembly with parts sourced globally rather than from LCSC only. For gerber/CPL export, stencil ordering, and BOM management, see the `bom` skill.

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Orchestrates an end-to-end de novo genome assembly project, routing each step to the right genome-assembly skill rather than restating it. Profiles the genome first (k-mer spectrum -> size, heterozygosity, ploidy), QCs reads, chooses an assembly path by data type (SPAdes for Illumina, Flye for noisy long reads, hifiasm for HiFi, metaFlye for communities), polishes only when needed, decontaminates, scaffolds with Hi-C, and finishes with three-axis QC (contiguity + completeness + correctness). Use when assembling a genome from raw reads and deciding which assembler, whether to polish, and how to prove the result is good.

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Profiles a genome from raw reads BEFORE assembly with a k-mer spectrum (KMC or Jellyfish histogram), then models it with GenomeScope2 to estimate genome size, heterozygosity, repeat content, and ploidy, and Smudgeplot to infer ploidy from heterozygous k-mer pairs (diploid AB vs triploid AAB vs tetraploid AABB). Covers choosing k via Merqury best_k.sh, the k-mer-coverage vs sequencing-coverage confusion, reading het/repeat/contamination/organelle peaks, why noisy ONT must not be used for counting, and how the estimate becomes the NG50 denominator, the Flye -g value, the hifiasm --hom-cov/purge setting, and the 1.5-2x-too-big haplotig sanity check. Use when starting any de novo assembly, deciding whether short reads can work, estimating genome size for an unknown organism, diagnosing ploidy, or sanity-checking an assembly's size against expectation.

The English summary is being prepared. Showing the original description.

Profiles a genome from raw reads BEFORE assembly with a k-mer spectrum (KMC or Jellyfish histogram), then models it with GenomeScope2 to estimate genome size, heterozygosity, repeat content, and ploidy, and Smudgeplot to infer ploidy from heterozygous k-mer pairs (diploid AB vs triploid AAB vs tetraploid AABB). Covers choosing k via Merqury best_k.sh, the k-mer-coverage vs sequencing-coverage confusion, reading het/repeat/contamination/organelle peaks, why noisy ONT must not be used for counting, and how the estimate becomes the NG50 denominator, the Flye -g value, the hifiasm --hom-cov/purge setting, and the 1.5-2x-too-big haplotig sanity check. Use when starting any de novo assembly, deciding whether short reads can work, estimating genome size for an unknown organism, diagnosing ploidy, or sanity-checking an assembly's size against expectation.

The English summary is being prepared. Showing the original description.

Find prebuilt WASM agents, software components packaged in WebAssembly format, through gallery browsing and keyword search. Install agents from their configurations, or export and publish your own agents to share with the community.

• Browse available community agents
• Find agents by keyword
• Install a prebuilt agent

Analyze compiled programs without running them by recognizing branches, loops, data structures, and common instruction patterns. Use disassembly and decompilation, which translate machine code into readable representations, to reconstruct program logic and document findings.

• Understand an unfamiliar executable
• Reconstruct branches and loops from assembly
• Infer data structures and function parameters