Results for “sequencing”

Plan database migrations before executing them: risk assessment, dependency mapping, multi-service sequencing, rollback budgets, and stakeholder communication plans. Use when deciding HOW to migrate, not when writing the actual DDL. NOT for: writing migration SQL (use database-migration-manager), data ETL pipelines (use data-migration-specialist), query optimization, or ORM configuration.

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Expert in color theory, palette harmony, and perceptual color science for computational photo composition. Specializes in earth-mover distance optimization, warm/cool alternation, diversity-aware palette selection, and hue-based photo sequencing. Activate on "color palette", "color harmony", "warm cool", "earth mover distance", "Wasserstein", "LAB space", "hue sorted", "palette matching". NOT for basic RGB manipulation (use standard image processing), single-photo color grading (use native-app-designer), UI color schemes (use vaporwave-glassomorphic-ui-designer), or color blindness simulation (accessibility specialists).

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Structures biological experiments so inference is valid by construction, covering Fisher's principles (randomization, replication, local control), the experimental-vs-observational unit distinction and pseudoreplication (Hurlbert 1984; Lazic 2018), randomization mechanics (complete, restricted, stratified, rerandomization, run-order), blocking layouts (randomized complete block, Latin square, incomplete block), factorial designs and interactions, and the split-plot/nested error strata hidden inside multi-batch genomics. Use when deciding the experimental unit and what counts as a replicate, planning randomization and run order, choosing a blocked/factorial/split-plot/nested layout, avoiding pseudoreplication in cell-culture or animal studies, or specifying the random-effects structure of the analysis model. For assigning samples to sequencing batches/lanes/plates and batch-effect correction see experimental-design/batch-design; for regulated clinical-trial randomization see clinical-biostatistics.

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Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.

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Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a mis-centered baseline, tuning CBS or HMM parameters, or understanding why a downstream CNV caller produced fragmented or shifted segments.

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Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than relative log2, when estimating purity and ploidy, calling LOH or copy-neutral LOH, resolving whole-genome doubling, running tumor-only allele-specific calling, or choosing among ASCAT, Sequenza, FACETS, and PureCN.

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Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.

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Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting ecDNA-driven oncogene amplification or therapy resistance, or selecting copy-number seeds for amplicon reconstruction.

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Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for visualization-only correction, and relationship to multi-condition design matrices. Use when combining screens for joint analysis, when passage cohort confounds biology, when DepMap-style panels need Chronos with batch covariates, when picking ComBat vs RUV, or when correction harms biology and should be replaced with explicit covariate modeling.

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Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincident independent molecules. Covers when single-strand consensus suffices vs when duplex is mandatory, the singleton/sensitivity tax at low input, and reading the insert-size histogram as a pre-analytical QC instrument. Use when processing plasma cfDNA reads before fragmentomics, ctDNA mutation calling, or tumor-fraction estimation.

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Fallback for general coding work that does not match any specific sextant sub-skill. Use for lightweight tasks: config changes, style fixes, utility functions, one-off scripts, or tasks too small to warrant a dedicated workflow. All dedicated sub-skills take priority over this one — check these first: sextant:fix-bug (broken behavior), sextant:debug (unknown bug location), sextant:add-feature (new functionality), sextant:modify-feature (changing existing behavior), sextant:review-code (evaluating code), sextant:write-tests (test coverage), sextant:refine-requirements (ambiguous scope), sextant:plan (multi-step sequencing), sextant:ship (release prep), sextant:migrate (cross-module upgrade), sextant:security (vulnerability audit). Only use this skill when none of the above match.

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Expert-level molecular biology knowledge. Use when working with DNA replication, transcription, translation, gene regulation, cloning, PCR, sequencing, CRISPR, epigenetics, or molecular techniques. Also use when the user mentions 'DNA replication', 'transcription', 'translation', 'gene expression', 'PCR', 'cloning', 'restriction enzyme', 'gel electrophoresis', 'Western blot', 'CRISPR', 'epigenetics', 'promoter', 'enhancer', or 'RNA splicing'.

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Use when sequencing market entry — geo / segment / vertical, beachhead selection, regulatory-delta. Triggers on 'should we enter market X', 'which segment first'.

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When shaping a non-trivial migration — rollout phases, dual-write windows, cutover sequencing, deprecation cycles — hands off to the framework-specific migration skill for DDL once locked.

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Use when sequencing a launch — alpha / beta / GA waves, audience-by-wave logic, narrative beats per wave, engineering-readiness gates. Triggers on 'plan the launch', 'sequence GA'.

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Load Remotion best practices for React video creation, including animations, composition setup, assets, audio, captions, sequencing, transitions, media metadata, Three.js, Tailwind, and rendering patterns. Use when creating, editing, debugging, or reviewing Remotion code.

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Apply when sequencing an addition, refactor, or rewrite. Remove dead weight, redundant validators, and stub references first, then build on the simpler base.

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Apply before writing logic: choosing core types and data structures, sequencing scaffold-vs-feature work, asking what concurrent actors share. Get the data structures right so downstream code becomes obvious.

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GStack CEO/founder-mode plan review for strategy, customer value, scope, sequencing, business risk, and whether the work should be done now.

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Load for Senior CTO critique, architectural audit, risk review, sequencing correction, or refinement of an existing implementation-plan triad; edits the requested plan/context/tasks in place without creating a worktree or review file. Not for open-ended CTO advice, product implementation, or implementation workspace setup.

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Codified expertise for production scheduling, job sequencing, line balancing, changeover optimisation, and bottleneck resolution in discrete and batch manufacturing.

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Plan or review FriendlyBet architecture, implementation, schema, data flows, scoring, provider integrations, static/PWA behavior, Supabase/RLS impact, migrations, automation, and technical sequencing. Use when a task asks how to build, refactor, generalize, integrate, test, or safely ship FriendlyBet code.

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