Results for “downstream”

Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4 (Marçais 2018 pairwise), minimap2 -x asm5/10/20 (Li 2018 fast pairwise), AnchorWave (Song 2022 WGD-aware), and Mauve / progressiveMauve (bacterial). Operates the HAL toolkit (Hickey 2013) for downstream extraction including halSynteny, halLiftover, halBranchMutations, and hal2maf. Use when constructing multi-species alignments for comparative-annotation projection (TOGA), synteny detection, conservation analyses (phyloP / PhastCons), or pangenome graph construction; selecting between reference-free (Cactus) and reference-anchored (LASTZ chains/nets) approaches; tuning sensitivity for closely vs distantly related genomes; or producing HAL files for genome-wide downstream tools.

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Cascade merge changes through a chain of dependent branches. Use when updating stacked/chained PRs, propagating changes from a parent branch to all downstream branches, or when the user mentions "cascade merge", "propagate changes", "update dependent branches", or "merge to downstream branches".

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Build whole-genome alignments using Progressive Cactus (Armstrong 2020 reference-free clade-level WGA), Minigraph-Cactus (Hickey 2024 pangenome-aware), LASTZ chain/net (UCSC pipeline), MUMmer4 (Marçais 2018 pairwise), minimap2 -x asm5/10/20 (Li 2018 fast pairwise), AnchorWave (Song 2022 WGD-aware), and Mauve / progressiveMauve (bacterial). Operates the HAL toolkit (Hickey 2013) for downstream extraction including halSynteny, halLiftover, halBranchMutations, and hal2maf. Use when constructing multi-species alignments for comparative-annotation projection (TOGA), synteny detection, conservation analyses (phyloP / PhastCons), or pangenome graph construction; selecting between reference-free (Cactus) and reference-anchored (LASTZ chains/nets) approaches; tuning sensitivity for closely vs distantly related genomes; or producing HAL files for genome-wide downstream tools.

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Maintain Paperclip Storybook examples by comparing them with shipped interfaces and the feature map. Update fixtures, classifications, and catalog references while preserving stable links and clearly identifying current examples, prototypes, historical work, and cases needing review.

• Reconciling Storybook examples after interface changes
• Updating mock data and API responses
• Classifying prototypes and historical examples

Turn notes or documents into a talk outline, page-by-page media choices, and a production brief for a separate slide-making skill. After rendering, check each slide against its planned purpose and generate revision instructions for up to three rounds.

• Turn notes or transcripts into a presentation outline
• Plan images, diagrams, and videos for each slide
• Prepare a production brief for HTML slides or PPTX

Hand accepted artifacts to the environment where work will continue, such as a code agent, desktop app, GitHub, or Figma. Record each destination in the artifact manifest, a tracking record that preserves earlier export history.

• Hand reviewed artifacts to Cursor, Claude Code, or Codex
• Return edited artifacts to their source Figma file
• Send accepted artifacts to GitHub through a PR

Send a single request to DeepSeek for summarization, information extraction, or simple classification. Receive the response and token usage as JSON for further processing, with structured status information when the API is unavailable.

• Summarizing text in a single request
• Extracting information from text
• Classifying text into simple categories

Dry-run one cycle of a sales agent workflow without calling language models. Validate the template and agent types, check budget reservations, generate agent prompts, and record a structured status summary for downstream automation.

• Demonstrating one cycle of a sales agent workflow
• Checking template validity and agent types
• Verifying budget caps and reservations

Inspect FCS files from flow cytometry, a method for measuring cell properties, using FlowIO. Extract measurement data into NumPy arrays, review channel metadata, export tables, and create FCS 3.1 files for downstream work.

• Inspect measurement settings and channel labels in FCS files
• Extract measurement data into NumPy arrays or CSV tables
• Read legacy FCS files containing multiple datasets

Prepare bulk RNA-seq sequencing files or quantification outputs for gene-level comparisons. Check sample information and data quality, configure processing workflows, and assemble validated count tables and metadata for downstream differential expression analysis with PyDESeq2.

• Preparing gene count tables from FASTQ files
• Configuring an nf-core/rnaseq workflow
• Combining Salmon, STAR, or featureCounts outputs

Examine container isolation in a CTF sandbox, a controlled security challenge environment. The skill checks kernel and runtime conditions, verifies whether an exploit crosses into host context, and preserves a minimal reproducible chain with evidence.

• Review container isolation settings in a CTF environment
• Check kernel exploit prerequisites
• Verify whether a trigger crosses the container boundary

Analyze binaries, malware samples, memory dumps, and packet captures in sandboxed security challenges. Trace program behavior, investigate crashes, and verify exploit conditions while preserving original files, decoded artifacts, and observable evidence for reproducible findings.

• Reverse engineer a binary’s structure and behavior
• Unpack a malware sample and separate its components
• Investigate crashes and verify exploit conditions

Examine Windows credential material in a CTF sandbox, including LSASS memory and Kerberos tickets. Distinguish stored secrets from credentials that actually work, and document the evidence linking their source to successful authentication or resulting privileges.

• Examining LSASS secrets and Windows logon sessions
• Checking whether recovered Kerberos tickets are usable
• Tracing DPAPI and SSP credential material

Analyze encrypted ZIP challenges in a CTF sandbox and use bkcrack to recover legacy ZipCrypto keys from known file contents. Create a decrypted archive, validate extraction, and preserve the commands and evidence needed to reproduce the result.

• Identify the encryption used by a ZIP archive
• Recover ZipCrypto keys from known file contents
• Validate and extract a decrypted archive

Solve sandboxed CTF security challenges by reconstructing encoding and encryption steps, extracting data hidden in media, and tracing mobile app signing or storage behavior. Preserve exact parameters and evidence to reproduce decoded content or signed requests.

• Reconstructing encoding and encryption chains in CTF challenges
• Extracting data hidden in images and other media
• Tracing APK or IPA request-signing logic

Trace uploaded files through extraction, conversion, parsing, and reconstruction of saved objects in a CTF sandbox, an isolated competition environment. Preserve original and derived files, distinguish visible validation from backend behavior, and document the smallest reproducible processing chain.

• Trace an uploaded file to its backend effect
• Investigate archive extraction and preview generation
• Compare visible validation with backend file handling

Compare how proxies and backend servers interpret HTTP requests in a CTF sandbox. Use paired requests and logs to pinpoint differences in paths, headers, or message boundaries, then document a minimal reproduction of unintended routing.

• Compare HTTP interpretation across proxies and backend servers
• Investigate path normalization and decoding differences
• Trace routing changes caused by ambiguous headers

Trace mailbox abuse in a CTF sandbox, a controlled security challenge environment. The skill connects OAuth permissions, forwarding rules, delegated access, and message logs to concrete mail effects, documenting the smallest reproducible sequence and supporting evidence.

• Trace how OAuth consent enables mailbox access
• Investigate forwarding and inbox rule effects
• Verify shared mailbox and delegated access

Investigate Kerberos delegation, which lets services act on another identity, in a CTF sandbox. Trace delegation settings, issued tickets, and service acceptance to document a reproducible trust path and the privileges it actually grants.

• Identifying constrained, unconstrained, or resource-based delegation
• Tracing S4U steps and issued authentication tickets
• Verifying ticket acceptance and resulting privileges

Trace how requests travel through a CTF sandbox, from hostnames and proxy rules to containers and processes. Compare headers and live traffic to identify which service handles a request and what changes its destination.

• Identify which container handles a request
• Check how Host and forwarded headers affect routing
• Trace path rewrites and WebSocket routing

Organize CTF investigations by mapping the supplied targets, tracing one minimal path, and selecting the relevant specialist workflow. Findings are grounded in observed behavior and reproducible evidence, with a clean baseline used for verification.

• Choosing an analysis path for a CTF challenge
• Tracing a minimal path through challenge infrastructure
• Packaging reproducible evidence for a solution

Investigate hidden data in CTF images, audio, video, and documents. Examine file structure and candidate hiding channels, then extract and reconstruct the payload while preserving intermediate files and reproducible steps.

• Inspecting metadata and data appended to media files
• Finding hidden data in image transparency or color channels
• Examining audio spectrograms and video frame differences

Investigate web applications in a CTF sandbox by tracing real browser requests, stored state, API calls, and background jobs. Compare successful and failing flows to explain authentication, routing, and differences between interface and server behavior.

• Trace authentication and session flows
• Compare browser state with server behavior
• Follow uploads and background jobs

Trace movement between Windows hosts in a CTF sandbox using credentials and Kerberos tickets, which carry authentication information. Connect recovered artifacts to the service that accepted them and document the resulting access or privileges.

• Trace movement between Windows hosts
• Identify services that accept recovered credentials
• Connect Kerberos tickets to resulting access