Results for “profiling”

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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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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Identify direct miRNA-target interactions from AGO HITS-CLIP, AGO-CLEAR-CLIP (chimeric reads), HEAP (Halo-Ago2 mouse), chimeric eCLIP / miR-eCLIP (deep miRNA-target profiling), or CLASH using chimeric-read processing pipelines, seed-pairing analysis, and 3' auxiliary pairing rules. Use when distinguishing direct miRNA targets from indirect, integrating CLIP-derived target maps with TargetScan / miRDB / DIANA predictions, applying canonical 7mer-8mer seed matching with 3' UTR context, or recovering miRNA-mRNA chimeras at scale.

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Analyzes CUT&RUN (Skene Henikoff 2017) and CUT&Tag (Kaya-Okur 2019) chromatin profiling data. Handles SEACR vs MACS2 peak calling (with the btaf375 2025 benchmark guidance), pA-MNase vs pA-Tn5 vs pAG-Tn5 chimera differences, E. coli spike-in carryover normalization, IgG-only control logic (no input), characteristic fragment-size signatures (25-75 bp for CUT&Tag), and lower depth requirements (5M reads typical vs 25M for ChIP). Use when calling peaks from CUT&RUN/CUT&Tag, scaling by E. coli spike-in carryover, choosing SEACR norm mode, or comparing CUT&RUN/Tag results to traditional ChIP.

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Investigates DAG incidents with a precise top event, timeline, competing hypotheses, barriers, propagation, and bounded recovery. NOT for automated root-cause classification, trace collection, or performance profiling.

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Learns from DAG execution history to improve future performance. Identifies successful patterns, detects anti-patterns, and provides recommendations. Activate on 'learn patterns', 'execution patterns', 'what worked', 'optimize based on history', 'pattern analysis'. NOT for failure analysis (use dag-failure-analyzer) or performance profiling (use dag-performance-profiler).

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Codified expertise for electricity and gas procurement, tariff optimization, demand charge management, renewable PPA evaluation, and multi-facility energy cost management. Informed by energy procurement managers with 15+ years experience at large commercial and industrial consumers. Includes market structure analysis, hedging strategies, load profiling, and sustainability reporting frameworks. Use when procuring energy, optimizing tariffs, managing demand charges, evaluating PPAs, or developing energy strategies.

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Optimize end-to-end application performance with profiling, observability, and backend/frontend tuning. Use when coordinating performance optimization across the stack.

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Optimize multi-agent systems with coordinated profiling, workload distribution, and cost-aware orchestration. Use when improving agent performance, throughput, or reliability.

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Apply systematic performance optimization techniques when writing or reviewing code. Use when optimizing hot paths, reducing latency, improving throughput, fixing performance regressions, or when the user mentions performance, optimization, speed, latency, throughput, profiling, or benchmarking.

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Optimize multi-agent systems with coordinated profiling, workload distribution, and cost-aware orchestration. Use when improving agent performance, throughput, or reliability.

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Analyze V8/Chrome CPU profiles (.cpuprofile) and DevTools trace files (Trace-*.json). Use when: profiling performance, investigating slow functions, comparing code paths, finding bottlenecks, analyzing timeToRequest, understanding call trees from sampling profiler data, analyzing layout/paint/rendering, investigating user timing marks.

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Expert-level browser automation, debugging, and performance analysis using Chrome DevTools MCP. Use for interacting with web pages, capturing screenshots, analyzing network traffic, and profiling performance.

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Trust scoring, agent discovery, profiling, wallet/identity lookup, contact, dispatch, and metadata reads/writes via 8K4 Protocol (ERC-8004). Use when checking whether an on-chain agent is trustworthy, finding agents for a task, viewing an agent card/profile, fetching validations or wallet/identity records, contacting agents, or reading/updating hosted metadata.

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Diagnoses .NET performance issues. dotnet-counters, dotnet-trace, dotnet-dump, flame graphs.

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Build comprehensive threat actor profiles using open-source intelligence (OSINT) techniques to document adversary motivations, capabilities, infrastructure, and TTPs for proactive defense.

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Map advanced persistent threat (APT) group tactics, techniques, and procedures (TTPs) to the MITRE ATT&CK framework using the ATT&CK Navigator and attackcti Python library. The analyst queries STIX/TAXII data for group-technique associations, generates Navigator layer files for visualization, and compares defensive coverage against adversary profiles. Activates for requests involving APT TTP mapping, ATT&CK Navigator layers, threat actor profiling, or MITRE technique coverage analysis.

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Optimize a measured performance problem when the user names a latency/load/Core Web Vitals/resource target or current profiling evidence identifies a bottleneck; do not trigger from generic implementation, review, or an unsupported suspicion that code may be slow.

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Analyze source data, tables, CSV/XLSX extracts, metrics, or experiment results with explicit data-authenticity checks. Use for profiling, cleaning assumptions, statistical summaries, segmentation, trend analysis, or "analyze this data"; do not use for spreadsheet file surgery, chart design only, database migrations, or claims without data provenance.

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