Tools & Automation

CLI tools, utilities, converters, workflow automation, and productivity helpers

skills in category: 47,643
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Showing 7,345–7,368 of 47,643 skills

Provision Bioinformatics SoftwareBAudit required bioinformatics command-line tools against Lmod or Environment Modules on Linux HPC clusters, resolve executable and version requirements, and reproducibly deploy missing software through a site-approved EasyBuild, Spack, Bioconda/micromamba, Apptainer, binary, or source-build workflow. Use when Codex must inspect module availability, diagnose a missing or wrong-version bioinformatics tool, install scientific software on Slurm/PBS clusters, publish or validate modulefiles, or pr...toolspythonshellVotes: 0GitHub stars: 3
Ncpgr LsfBNCPGR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。toolspythonshellVotes: 0GitHub stars: 3
Ncpgr Data ManageA集群数据管理 Skill —— 涵盖数据使用规范、压缩优化、数据共享（ACL）、文件扫描与清理、文件完整性校验、genozip 基因组压缩等全流程。Use when the user asks about: managing data on the HPC cluster, compressing genomic files (fq/bam/vcf), sharing data between users/groups, scanning for large files or cleaning up disk space, checking file integrity (md5/gzip/bam), using genozip, checking disk quota, or any data lifecycle management task on the NCPGR HPC cluster.toolsbashtestingVotes: 0GitHub stars: 3
Lsf Memory ScalingALSF 作业内存不足时的调整技能。当作业因内存不够被挂起(SSUSP)或终止(EXIT/MEMLIMIT)时，通过调整 bsub -n 的节点（核数/slot）数量来扩大可用内存——可用运行内存 ≈ 5GB × 申请节点数。当用户说内存不足、作业被杀、OOM、需要更大内存，或排查 EXIT/SSUSP 作业时，配合 lsf-ncpgr skill 一起使用。toolsVotes: 0GitHub stars: 3
Riboseq PipelineAEnd-to-end Ribo-seq analysis from FASTQ to translation efficiency and ORF detection. Use when analyzing ribosome profiling data to study translation.toolspythonbashVotes: 0GitHub stars: 3
Edna PipelineAEnd-to-end eDNA metabarcoding from raw amplicons to community ecology. Covers QC, primer removal (mandatory before DADA2 filterAndTrim), denoising with OBITools3 v3 (obi stats plural; DMS-based) or DADA2 ASVs (Callahan 2017), decontam combined method as screening-not-classifier (Davis 2018), tag-jumping with NovaSeq 10x MiSeq caveat (Schnell 2015), Hill-number effective species counts with coverage-based rarefaction (Jost 2006; Chao & Jost 2012; doubling rule), beta-diversity decomposition wi...toolsgobashVotes: 0GitHub stars: 3
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Vcf StatisticsAGenerate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluating variant quality, comparing samples, or summarizing VCF contents.toolspythongoVotes: 0GitHub stars: 3
Format ConversionAConvert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.toolspythongoVotes: 0GitHub stars: 3
Filter SequencesAFilter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted records, or selecting by specific criteria.toolspythongoVotes: 0GitHub stars: 3
Alignment Free QuantAQuantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Salmon or kallisto.toolspythongoVotes: 0GitHub stars: 3
Ribosome PeriodicityAValidate Ribo-seq data quality by checking 3-nucleotide periodicity and calculating P-site offsets. Use when assessing library quality or determining read offsets for downstream analysis.toolspythongoVotes: 0GitHub stars: 3
Riboseq PreprocessingAPreprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when preparing Ribo-seq reads for downstream analysis of translation.toolspythongoVotes: 0GitHub stars: 3
Umi ProcessingAExtract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes UMIs and accurate molecule counting is needed, such as in single-cell RNA-seq, low-input RNA-seq, or targeted sequencing to distinguish PCR from biological duplicates.toolspythongoVotes: 0GitHub stars: 3
Adapter TrimmingARemove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequences. Use when FastQC shows adapter contamination or before alignment of short reads.toolsbashapiVotes: 0GitHub stars: 3
Bwa AlignmentAAlign DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short reads to a reference genome.toolsgobashVotes: 0GitHub stars: 3
Reference PanelsADownload, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels. Use when setting up imputation infrastructure or selecting appropriate reference panels for target populations.toolsjavabashVotes: 0GitHub stars: 3
Qiime2 WorkflowAQIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when preferring CLI over R, needing reproducible provenance, or working within QIIME2 ecosystem.toolspythongoVotes: 0GitHub stars: 3
Bismark AlignmentABisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.toolsbashtestingVotes: 0GitHub stars: 3
Merip PreprocessingAAligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq c_curve / lc_extrap, and the explicit do-NOT-deduplicate convention for ...toolspythonrustVotes: 0GitHub stars: 3
Lsf SkillsBNCPGR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。toolspythonshellVotes: 0GitHub stars: 3
Lsf NcpgrBNCPGR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。toolspythonshellVotes: 0GitHub stars: 3
Workflow InitAInstall and configure Vercel Workflow SDK before it exists in node_modules. Use when the user asks to "install workflow", "set up workflow", "add durable workflows", "configure workflow sdk", or "init workflow" for Next.js, Express, Hono, Fastify, NestJS, Nitro, Nuxt, Astro, SvelteKit, or Vite.toolsgonextjsVotes: 0GitHub stars: 2,447
Internal Dev WorkbenchBSpin up a portless + tmux dev session for the Workflow SDK that gives each git worktree isolated `<branch>.<name>.localhost` URLs for the Next.js workbench and the observability UI, plus a Claude statusline that surfaces those URLs. Use only when the user asks for a "portless dev session", a "tmux dev layout for workflow", "worktree-isolated dev URLs", or wants to wire workflow dev URLs into the Claude statusline. Do not activate for the generic "start the dev server" / "run pnpm dev" task.toolsrustshellVotes: 0GitHub stars: 2,447
3380p Test Plan To ProgramA根据详细测试计划生成、整理或修订 Chroma 3380P ATE 测试程序草稿。用于把测试计划翻译成可评审的 `.pln`、必要 `.dec` 或 `.pat`，尤其适用于 PLN 测试项、supply sweep threshold、register setup helper、WRITE_PAT_MEM 动态改 pattern、capture readback、DC measure、pattern 执行和 multi-site result/judge 逻辑。toolsVotes: 0GitHub stars: 2