Other skills

NCPGR高性能计算集群软件使用注意事项与优化指南。聚焦各软件的坑点、加速技巧、资源节省建议与软件选型推荐。当用户询问集群上如何高效使用软件、编写LSF作业、或需要软件选型建议时使用。

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Select, document, download, and checksum-verify the most appropriate NCBI reference genome on an HPC cluster. Use whenever an analysis needs a reference genome, genome FASTA, genome annotation, assembly accession, or genome index and no exact approved assembly is already available; when a user asks to fetch a species genome from NCBI; or when a pipeline must resolve and cache a reproducible reference assembly on a remote cluster.

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Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.

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NCPGR高性能计算集群LSF作业调度系统使用指南。用于提交、管理和监控LSF批处理作业，包括串行作业、多线程作业、MPI并行作业、GPU作业、数组作业等。当用户需要编写LSF作业脚本、提交计算任务、查询作业状态、调整作业参数或排查作业问题时使用此skill。

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View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignment file structure.

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生成图文并茂的分析报告/实验报告/质检报告（固定模版）。当用户要求"生成报告/总结报告/实验报告/质检报告/QC报告"，或分析流程收尾需要交付报告时使用。报告必须基于真实分析输出，包含固定章节结构、关键指标表格和真实结果图。

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Align protein structures using Foldseek 3Di, TM-align, US-align, DALI, or Foldmason for structural MSA. Predict, score, and superpose backbone coordinates when sequence identity is below the twilight zone or remote-homology detection is required. Use when sequence MSA fails (<25% identity), when the dark proteome is the target, when AlphaFoldDB / ESM Atlas search is needed, or when structural superposition is the goal.

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Map nucleosome center positions, occupancy, and fuzziness from ATAC-seq fragment-size patterns using NucleoATAC, ATACseqQC, DANPOS3, or scprinter. Use when characterizing nucleosome organization at promoters and enhancers, calling +1/-1 nucleosomes flanking NFRs, generating V-plots for chromatin structure visualization, or comparing nucleosome positioning between conditions.

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Use this skill when documenting supervisor reasonable-suspicion training for Part 382 compliance. Covers what to log, what to retain, and what training providers to use.

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Use this skill when selecting a TPR-registered Training Provider for behind-the-wheel ELDT training. Covers the registry, evaluation criteria, and common pitfalls.

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Use this skill when the user asks about weigh-station bypass services — Drivewyze, PrePass, BestPass, NORPASS, OOIDA toll savings — how they work, eligibility criteria, costs, and how they tie into CSA scores. Reference each provider's coverage area + pricing.

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Use this skill when the user asks about refrigerated (reefer) trucking — cold chain compliance, FDA temperature recording requirements, Sanitary Transportation Rule (STR / 21 CFR 1.900-1.934), commodity-specific temperature ranges, refrigeration unit operation, temperature recorder calibration, and how a load is challenged if temperature deviates. Cite 21 CFR Part 1 Subpart Q.

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Use this skill to understand FMCSA tire tread depth requirements. Covers steer tires (4/32 minimum) and other axles (2/32 minimum), and how to measure correctly.

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Use when a carrier asks how to spec a new tractor — engine choice (X15 vs DD16 vs PACCAR MX), transmission (manual vs automated manual vs automatic), axle ratio, sleeper size, fuel tanks, aerodynamic options, electronic features, warranty, fleet-spec vs premium-spec tradeoffs, and how spec choices affect resale value.

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Use this skill when the user asks about passenger-carrying CMVs — buses, motorcoaches, charter operations, school buses, limousines, shuttle services. Covers different HOS rules (10-hour driving / 15-hour on-duty / no 34-restart), Class C CDL with P endorsement, S endorsement for school bus, FMCSA Hours-of-Service for passenger vehicles, $5M insurance minimum, BMC-32 filing, accessibility requirements, and how passenger ops differ from property. Cite 49 CFR 395.5 + 387.33.

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Use this skill when the user asks about CMV oilfield operations — the 24-hour restart exemption (49 CFR 395.1(d)), oilfield-specific HOS rules, hot oil hauling, specialty equipment (winch trucks, kill trucks, frac sand haulers, water haulers), Texas Railroad Commission permitting, oilfield insurance specifics, and how oilfield operations differ from standard OTR trucking. Cite 49 CFR 395.1(d).

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Use when an owner-operator (1099 or LLC/S-corp) asks how to lower their tax bill, what they can deduct, per diem treatment, depreciation choices (Section 179, bonus, MACRS), quarterly estimated payments, S-corp salary vs distributions, retirement plan options (SEP-IRA, Solo 401(k)), or recordkeeping requirements. Covers federal income tax + self-employment tax basics; not state-specific.

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Use this skill to understand defensive driving course expectations for CMV drivers. Covers federal vs state vs carrier-specific requirements.

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Use this skill when the user asks the cost of pulling a Motor Vehicle Record (MVR) in a specific state, or wants to compare MVR fees across multiple states, or is budgeting annual compliance costs for a multi-state fleet. Reference the canonical fee table below; flag that fees change (re-verify with state DMV before annual budget planning).

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Use this skill to understand record retention requirements for currently-employed drivers. Covers DQF, HOS, vehicle records, and D&A specific periods.

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Use when a carrier asks about trailer types — dry van, reefer, flatbed, step-deck, conestoga, tanker, dump, lowboy, intermodal chassis, auto-hauler. Covers length / weight rules, common specs, reefer unit options (Carrier vs Thermo King), liftgate options, kingpin setting, and trailer-to-tractor matching.

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Use when a carrier or driver asks about winter trucking, snow chain requirements, hot-weather precautions, summer tire failures, fuel additive use (anti-gel), idle management in extreme temperatures, weight restrictions in spring thaw, or how seasonal demand patterns affect freight rates and capacity.

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Use this skill when the user asks about the financial differences between being an owner-operator vs company driver — gross pay, expenses, net pay, capital requirements, risk tolerance, lifestyle, and how to evaluate the path. Reference industry pay surveys.

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Use when a carrier is evaluating ELD / telematics / dashcam platforms and needs an objective comparison of Samsara, Motive (formerly KeepTruckin), and Geotab. Covers ELD compliance, AI dashcams, driver scoring, integrations, pricing structure, and which fleet profile suits which platform.

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