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.

Applies the TAM/SAM/SOM market sizing framework to guide decision-making, structure analysis, and produce actionable recommendations for product research.

Deterministic mathematical computation using SymPy. Use for ANY math operation requiring exact/verified results - basic arithmetic, algebra (simplify, expand, factor, solve equations), calculus (derivatives, integrals, limits, series), linear algebra (matrices, determinants, eigenvalues), trigonometry, number theory (primes, GCD/LCM, factorization), and statistics. Ensures mathematical accuracy by using symbolic computation rather than LLM estimation.

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

Full-stack task execution pipeline — discovers tools via semantic search, routes to the right agent, then executes via GODMODE. Chains manus-tool-discovery → manus-orchestrator → godmode-system in sequence.

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.

Writes or updates a HANDOFF.md file in the project root to capture goal, progress, and next steps for a fresh agent to continue in-progress work.

Query and analyze SEC filings using EdgarTools

Create a SAM.gov search monitor from a pursuit or expiring row — persists to Pipeline and writes sam_monitor.md in the pursuit folder. Primary admin rote task for capture managers watching recompetes.

Generates speech from text using ElevenLabs TTS with local playback, supporting voice selection, pronunciation rules, and audio tags.

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.

Identifies operational toil, prioritizes automation by ROI, and provides patterns for self-healing systems and runbook automation.

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.

Use when converting NCBI dbSNP docsum XML into flat tabular rows through the bundled `snp2hgvs | hgvs2spdi | spdi2tbl` pipeline.

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.

Simulator.Company financial management specialist. Use when the user wants to manage financial and metric accounts on actors (balances, counters, plan vs fact), record transactions, transfer value between accounts, work with currencies and account-name categories, track non-financial metrics, read balances and turnover, tag accounts for grouping, or set up account triggers (balance / transaction-count / data-field alerts). Activate when the user mentions "record transaction", "transfer funds", "account balance", "financial tracking", "depreciation", "expense", "budget", "counter", "mileage tracking", "account tag", "account trigger", "balance alert", "запиши транзакцію", "переказ коштів", "баланс рахунку", "лічильник", "пробіг", "тег рахунку", "тригер на рахунок", "запиши транзакцию", "перевод средств", "баланс счёта", "счётчик", "пробег", "тег счёта", "триггер на счёт". Accounts attach to ACTORS — use `simulator-actors` to create/find the actor first; for sharing an account use `simulator-access`; for dashbo

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 this skill when conditioning, loading, preparing, or labeling signal data for analysis or ML training. Covers: cleaning a single signal (fill gaps, remove drift, deoutlier, denoise, resample/align a time base) BEFORE analysis; building a `signalDatastore` pipeline; creating a `labeledSignalSet` for Signal Labeler; deriving labels (filename, folder, in-file, ROI, time-frequency ROI); stratified train/val/test splits; framing long signals; parallel processing; and shaping datastore output for `trainnet`. Triggers include "clean up this signal", "remove drift / detrend", "fill gaps", "remove spikes / outliers", "denoise", "resample to a uniform rate", "align channels", "labels from filenames", "stratified split", "prepare for Signal Labeler", and function names like `fillgaps`, `fillmissing`, `detrend`, `filloutliers`, `smoothdata`, `resample`, `synchronize`, `signalDatastore`, `labeledSignalSet`, `filenames2labels`, `folders2labels`, `splitlabels`, `framesig`, `framelbl`, `createDatastores`.

Automates the collection of suspicious files from endpoints and email gateways, submission to sandbox and multi-engine scanners, and generation of verdicts with IOCs for SIEM integration.

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.

Validates inputs, generates samplesheets and launch scripts, and optionally executes nf-core/pacsomatic matched tumor-normal workflows from BAM files, supporting local runs and scheduler submission (LSF/Slurm/PBS/SGE).