Results for “samtools”

Sets up Pawbytes Tools module in a project. Use when the user requests to 'install paw tools', 'configure Pawbytes Tools', or 'setup utility tools'.

Use when working with NCBI ASN.1 module files, schema exports, or ASN.1/XML conversion tasks that require the `datatool` command.

Use when converting ACE assembly files into SAM while preserving legacy ACE-specific padded or contig-sequence behavior.

Process and analyze high-throughput sequencing data with deepTools for quality control, normalization, comparison, and publication-quality visualizations of ChIP-seq, RNA-seq, and ATAC-seq experiments.

Calculate TAM, SAM, and SOM with explicit assumptions, methods, and caveats for market sizing.

Use when paired-end reads need to be reordered so mates appear consecutively, or when preparing BAM files for featureCounts by adding dummy reads for singletons.

Query and analyze SEC filings using EdgarTools

Remote-control tmux sessions for interactive CLIs by sending keystrokes and scraping pane output.

Sample Text Processor

Use when performing genome arithmetic on interval files (BED, BAM, BEDGRAPH), including intersection, merging, coverage, format conversion, or sequence extraction.

NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

Use when working with VCF/BCF variant files for indexing, manipulation, analysis, or variant calling.

Skill for the Sessions area of paddock. 50 symbols across 13 files.

Remote-control tmux sessions for interactive CLIs by sending keystrokes and scraping pane output.

Unified math capabilities - computation, solving, and explanation. I route to the right tool.

Skill for the Panels area of paddock. 727 symbols across 76 files.

Find adjacent vendors and subs (not top market primes) who fill a capability gap against a displacement target using USASpending flows and SAM entity signals. Use when user defines a teaming gap and wants vault-ready partner shortlist with citations.

Search SAM.gov for live notices matching a pursuit row (agency, incumbent, NAICS keywords) and save results to sam_scan.md. Use for admin monitor setup, presolicitation watch, or when user asks what is live on SAM for an expiring contract.

Use when you need to perform quality control analysis on high-throughput sequencing data (fastq, bam, sam, or fast5 files) to identify potential problems before downstream analysis.

Worktree-first dev environment manager for issues, PRs, and features with optional tmux sessions

Configure Okta as a SAML 2.0 Identity Provider and implement SP-initiated and IdP-initiated SSO flows with attribute mapping, assertion encryption, and security hardening.

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Simulator.Company graph structure specialist. Use when the user wants to build, edit, analyze, inspect, or ask questions about business process graphs, flowcharts, algorithms, actors (nodes), links (edges), or layers (visual views) in Simulator.Company. Trigger on any of these intents: — Creating: "create graph", "build flowchart", "new diagram", "add actor", "add block to graph", "create algorithm", "draw flowchart", "digital twin", "create process on graph", "build process diagram", "FlowchartBlock", "startStop", "predefinedProcess". — Editing: "edit graph", "update actor", "rename node", "change color", "move actor", "add step to flowchart", "modify diagram", "restructure process", "add edge", "remove link", "reorder steps", "update layer". — Syncing: "push graph", "pull graph", "sync graph", "push changes", "apply edits to layer". — Querying / analysis: "what actors are on this layer", "show me the graph", "who is connected to", "find actor", "list nodes", "describe the process", "analyze the flowchart",

Remote-control tmux sessions for interactive CLIs by sending keystrokes and scraping pane output.

Central utility skill for GSD operations. Provides config parsing, slug generation, timestamps, path operations, and orchestrates calls to other specialized skills. Acts as the unified entry point that the original gsd-tools.cjs provided via its lib/ modules (commands, config, core, init).

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

Configure and maintain Python projects, dependencies, packaging, environments, linting, formatting, type checking, testing, builds, and publishing. Use for pyproject.toml, an existing repository toolchain, or repository-level Python tooling work, not for a standalone script.

Anti-distillation defense for employee Skills. Clean your skill files to look complete but with core proprietary knowledge neutralized. Use when user wants to protect trade secrets, sanitize forced knowledge transfers, or create safe-to-submit skill documents.

Simulator.Company chart and dashboard specialist. Use when the user wants to create, configure, or query charts (line, bar, area), dashboards, or financial time-series visualisations on a graph layer. Trigger on any of these intents: — Creating: "create chart", "add chart", "create dashboard", "add dashboard", "build visualisation", "chart на графе", "график с данными", "дашборд", "show metrics on graph", "visualise account data", "plot actor balances". — Configuring: "change chart type", "switch to bar chart", "update chart range", "use last day", "show turnover", "change time range", "filter chart actors". — Querying: "get chart data", "show dashboard", "what charts are on this layer", "fetch chart metrics", "dashboard data".

Safe Notes Skill

Remote-control tmux sessions for interactive CLIs by sending keystrokes and scraping pane output.

导出/导入/分享/同步 Hermes Skills。use `hermes-skill` command.

Use when searching protein sequences against profile hidden Markov models (HMMs) such as Pfam or other HMM databases.