Results for “duplicates”

Computes and interprets sequencing read depth and coverage over a genome, windows, or target regions with mosdepth (windowed depth, cumulative distribution, --quantize callable BEDs), bedtools genomecov/coverage (bedGraph tracks, per-target stats), samtools depth/coverage (per-base depth, per-contig depth+breadth). Covers the breadth-vs-mean distinction, the cumulative-coverage curve, evenness (CV/Fano/fold-80/Gini), what each tool silently counts (duplicates, secondary/supplementary, MAPQ, read span vs fragment, mate-overlap), the samtools-depth 8000-cap version trap, and the bedtools coverage -a/-b orientation flip. Use when assessing sequencing adequacy, building coverage tracks, computing breadth at a depth threshold, defining callable regions, or QCing target-capture uniformity.

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Turns Hi-C/Micro-C FASTQ into a deduplicated, filtered .pairs file with pairtools and decides whether the library worked. Covers the bwa mem -SP5M / bwa-mem2 / chromap --preset hic alignment idiom (mates mapped as independent single-end reads), pairtools parse vs parse2 and the walks-policy choice (5unique pairwise vs all for Pore-C/Micro-C concatemers), pair-type classification (keep UU and rescued UC), dedup (PCR vs optical/by-tile), select by pair_type/MAPQ/distance, restriction-fragment handling (restrict, Arima dual-enzyme, Micro-C/DNase fragment-free), and allele-specific phasing (pairtools phase to two coolers). The library-QC decision uses % long-range cis as the one-number quality metric, trans as the noise floor, orientation balance as fragment-map-free dangling-end/self-circle QC, and % duplicates as a complexity proxy. Use when processing Hi-C/Micro-C/Omni-C reads into pairs, judging library quality, handling multi-enzyme or restriction-agnostic protocols, or generating allele-specific contacts.

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Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.

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Discipline an AI agent needs to work an issue/task tracker (Jira, Linear, GitHub Issues) as the shared source of truth: pull the right next item instead of inventing work, search before creating to avoid duplicates, write actionable items with checkable acceptance criteria, keep status transitions honest, and link work to items via branches/PRs/commits so progress is legible. Use when an agent picks up tracker work, files a new issue, updates status, or closes an item. NOT for authoring the PR itself (use agent-pr-authoring), roadmap-level planning and prioritization (use legible-roadmap-with-sidequests), or the mechanics of multiple agents coordinating on the same codebase (use multi-agent-coordination).

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Turn a large dataset (an existing oversized Coval test set, an export of past conversations, or a CSV/JSON of cases) into a small, high-signal Coval test set by removing duplicates, identifying unique scenarios, and selecting a representative, failure-weighted subset — then bulk-loading it with no row cap. Use when the user says "I have thousands of cases", "dedupe my test set", "my test set is too big", "turn this dataset into a test set", "pick representative scenarios", or "my CSV import only kept 10 / uploaded everything".

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Moves a person's whole Notion workspace into AI Matrx using only the AI Matrx and Notion connectors — every page and sub-page becomes an AI Matrx page (a Space) with its blocks, icons, covers, files and comments, and every database becomes a real table with typed columns, links, roll-ups, row pages, templates and views. Safe to run again; nothing duplicates. Use when the person says "move my Notion into AI Matrx", "copy my Notion", "import my Notion", or anything like it.

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[70] CLOSE. Manage task lifecycle with correct statuses and no duplicates. Ensure each task has one status, artifacts match claims, and no task appears in multiple places. Use when managing task lists, updating progress, or ensuring task tracking integrity across systems.

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Finds open GitHub PRs with security and priority-high labels, links each to its issue, detects duplicates (multiple PRs fixing the same issue), and presents a table of review candidates. Use when looking for the next PR to review. Trigger keywords - find pr, find review, next pr, pr to review, duplicate pr, security pr.

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Use this skill when importing Excel, CSV, or pasted rows with nuxt-ui-tools as a package consumer. Covers defineSpreadsheetSchema (typed context, chained text/number/date/boolean/select columns, columns depending on the columns above (options, defaults, rules per row), groups and dynamic groups built from the context, exact matching, option sources shared with forms, unknown-value policies, rules and levels, validate, row identity with duplicates and stored records, output), useSpreadsheetImport (headless models, onSubmit with batches and rejections), the UiSpreadsheetImport* parts, useSpreadsheetSteps with custom steps, and the ready-made UiSpreadsheetImport wizard.

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Intelligently organizes your files and folders across your computer by understanding context, finding duplicates, suggesting better structures, and automating cleanup tasks. Reduces cognitive load and keeps your digital workspace tidy without manual effort.

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Audits project dependencies for outdated packages, duplicates, heavy/problematic libraries, security vulnerabilities, and risky version combinations. Generates prioritized reports with security, performance, and maintainability insights, upgrade paths, and safe pinning recommendations. Use when users request dependency audits, package updates, security checks, or dependency optimization.

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Two-phase Apollo.io prospecting: free People Search to discover ICP-matching leads, then selective enrichment to reveal emails/phones (credits per contact). Deduplicates against CRM (Google Sheets). Supports Apollo API and MCP tools.

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Gates whether a new test should exist and forces it to be efficient, protecting CI from low-value test bloat. Use before any change to what a pytest, Jest, or Playwright test asserts or sets up, down to one fixture or one assertion added to an existing block. Front-loads the value bar (every test must catch a realistic regression no existing test already catches; extend the nearest existing test before writing a new standalone one; test behavior through the public interface, not implementation details; collapse near-duplicates into parameterized cases) and the efficiency bar (deterministic, isolated, fast; pick the cheapest test level; Django TestCase over TransactionTestCase; no sleeps, no real network; no time bombs from absolute dates left to age against the real clock; no database a test never uses). Includes a "don't write it" decision tree. For fixing an existing flaky test use `/fixing-flaky-tests`; after this gate says a Playwright test is warranted, use `/playwright-test` for mechanics.

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