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Claude Skills by mdbabumiamssm
github.com/mdbabumiamssm1,578 skills3 installs3,530 views
- Consensus Sequences--> --- name: bio-consensus-sequences description: Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes. tool_type: cli primary_tool: bcftools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Apply variants to reference FASTA using bcftools consensus.Votes: 0GitHub stars: 6
- Deepvariant--> --- name: bio-variant-calling-deepvariant description: Deep learning-based variant calling with Google DeepVariant. Provides high accuracy for germline SNPs and indels from Illumina, PacBio, and ONT data. Use when calling variants with DeepVariant deep learning caller. tool_type: cli primary_tool: DeepVariant measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Filtering Best Practices--> --- name: bio-variant-calling-filtering-best-practices description: Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels. Use when filtering variants using GATK best practices. tool_type: mixed primary_tool: bcftools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Gatk Variant Calling--> --- name: bio-gatk-variant-calling description: Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR). Use when calling variants with GATK HaplotypeCaller. tool_type: cli primary_tool: gatk measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- GATK HaplotypeCall...Votes: 0GitHub stars: 6
- Joint Calling--> --- name: bio-variant-calling-joint-calling description: Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies, population genetics, and leveraging VQSR. Use when performing joint genotyping across multiple samples. tool_type: cli primary_tool: GATK measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Call variants jointly across multi...Votes: 0GitHub stars: 6
- Structural Variant Calling--> --- name: bio-variant-calling-structural-variant-calling description: Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations that are too large for standard SNV callers. Use when detecting structural variants from short-read data. tool_type: cli primary_tool: manta measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_fi...Votes: 0GitHub stars: 6
- Variant Annotation--> --- name: bio-variant-annotation description: Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance. Use when annotating variants with functional and clinical information. tool_type: mixed primary_tool: VEP measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Variant Calling--> --- name: bio-variant-calling description: Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments. tool_type: cli primary_tool: bcftools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Call SNPs and indels from aligned reads using bcftools.Votes: 0GitHub stars: 6
- Variant Normalization--> --- name: bio-variant-normalization description: Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream analysis. tool_type: cli primary_tool: bcftools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Left-align indels and split multiallelic sites using bcftools norm.Votes: 0GitHub stars: 6
- Vcf Basics--> --- name: bio-vcf-basics description: View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting specific fields, or understanding VCF format structure. tool_type: cli primary_tool: bcftools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- View and query variant files using bcftools and cyvcf2.Votes: 0GitHub stars: 6
- Vcf Manipulation--> --- name: bio-vcf-manipulation description: Merge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restructuring VCF data. tool_type: cli primary_tool: bcftools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Merge, concat, sort, and compare VCF files using bcftools.Votes: 0GitHub stars: 6
- Vcf Statistics--> --- name: bio-vcf-statistics description: Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluating variant quality, comparing samples, or summarizing VCF contents. tool_type: cli primary_tool: bcftools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Generate statistics and quality metrics using bcftools.Votes: 0GitHub stars: 6
- VarCADD--> --- name: varcadd-pathogenicity description: Variant Scorer keywords: - variant-interpretation - CADD - pathogenicity - genomics - prediction measurable_outcome: Return pathogenicity scores for a VCF of 1000 variants within 2 minutes, flagging top 1% deleterious hits. license: Non-Commercial metadata: author: Genome Medicine 2025 version: "1.0.0" compatibility: - system: Python 3.9+ allowed-tools: - run_shell_command - read_file --- Genome-wide pathogenicity prediction leveraging standing...Votes: 0GitHub stars: 6
- Cnv Annotation--> --- name: bio-copy-number-cnv-annotation description: Annotate CNVs with genes, pathways, and clinical significance. Use when interpreting CNV calls or identifying affected genes from copy number analysis. tool_type: mixed primary_tool: bedtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Cnv Visualization--> --- name: bio-copy-number-cnv-visualization description: Visualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or other callers. Use when creating genome-wide CNV plots, sample heatmaps, or chromosome-level visualizations. tool_type: mixed primary_tool: matplotlib measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Cnvkit Analysis--> --- name: bio-copy-number-cnvkit-analysis description: Detect copy number variants from targeted/exome sequencing using CNVkit. Supports tumor-normal pairs, tumor-only, and germline CNV calling. Use when detecting CNVs from WES or targeted panel sequencing data. tool_type: cli primary_tool: cnvkit measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Gatk Cnv--> --- name: bio-copy-number-gatk-cnv description: Call copy number variants using GATK best practices workflow. Supports both somatic (tumor-normal) and germline CNV detection from WGS or WES data. Use when following GATK best practices or integrating CNV calling with other GATK variant pipelines. tool_type: cli primary_tool: gatk measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Base Editing Analysis--> --- name: bio-crispr-screens-base-editing-analysis description: Analyzes base editing and prime editing outcomes including editing efficiency, bystander edits, and indel frequencies. Use when quantifying CRISPR base editor results, comparing ABE vs CBE efficiency, or assessing prime editing fidelity. tool_type: python primary_tool: CRISPResso2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Batch Correction--> --- name: bio-crispr-screens-batch-correction description: Batch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch-aware analysis. Use when combining screens from multiple batches or correcting systematic technical variation. tool_type: python primary_tool: scipy measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Crispresso Editing--> --- name: bio-crispr-screens-crispresso-editing description: CRISPResso2 for analyzing CRISPR gene editing outcomes. Quantifies indels, HDR efficiency, and generates comprehensive editing reports. Use when analyzing amplicon sequencing data from CRISPR editing experiments to assess editing efficiency. tool_type: cli primary_tool: CRISPResso2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Hit Calling--> --- name: bio-crispr-screens-hit-calling description: Statistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and resistance genes. Use when identifying significant genes from screen count data after QC passes. tool_type: mixed primary_tool: bagel2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Jacks Analysis--> --- name: bio-crispr-screens-jacks-analysis description: JACKS (Joint Analysis of CRISPR/Cas9 Knockout Screens) for modeling sgRNA efficacy and gene essentiality. Use when analyzing multiple CRISPR screens simultaneously or when accounting for variable sgRNA efficiency across experiments. tool_type: python primary_tool: JACKS measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- JACKS jointly models ...Votes: 0GitHub stars: 6
- Library Design--> --- name: bio-crispr-screens-library-design description: CRISPR library design for genetic screens. Covers sgRNA selection, library composition, control design, and oligo ordering. Use when designing custom sgRNA libraries for knockout, activation, or interference screens. tool_type: python primary_tool: crispor measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Mageck Analysis--> --- name: bio-crispr-screens-mageck-analysis description: MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) for pooled CRISPR screen analysis. Covers count normalization, gene ranking, and pathway analysis. Use when identifying essential genes, drug targets, or resistance mechanisms from dropout or enrichment screens. tool_type: cli primary_tool: mageck measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file -...Votes: 0GitHub stars: 6
- Screen Qc--> --- name: bio-crispr-screens-screen-qc description: Quality control for pooled CRISPR screens. Covers library representation, read distribution, replicate correlation, and essential gene recovery. Use when assessing screen quality before hit calling or diagnosing poor screen performance. tool_type: python primary_tool: pandas measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Assembly Polishing--> --- name: bio-genome-assembly-assembly-polishing description: Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka). Essential for improving long-read assembly accuracy. Use when improving assembly accuracy with polishing tools. tool_type: cli primary_tool: Pilon measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Improve assembly ac...Votes: 0GitHub stars: 6
- Assembly Qc--> --- name: bio-genome-assembly-assembly-qc description: Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers. Use when evaluating assembly completeness and quality. tool_type: cli primary_tool: QUAST measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Evaluate genome assembly quality with cont...Votes: 0GitHub stars: 6
- Contamination Detection--> --- name: bio-genome-assembly-contamination-detection description: Detect contamination and assess genome quality using CheckM, CheckM2, GTDB-Tk, and GUNC for metagenome-assembled genomes and isolate assemblies. Use when checking assemblies for contamination. tool_type: cli primary_tool: CheckM2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Hifi Assembly--> --- name: bio-genome-assembly-hifi-assembly description: High-quality genome assembly from PacBio HiFi reads using hifiasm with phasing support. Use when building reference-quality diploid assemblies from HiFi data, especially with trio or Hi-C phasing for fully resolved haplotypes. tool_type: cli primary_tool: hifiasm measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Long Read Assembly--> --- name: bio-genome-assembly-long-read-assembly description: De novo genome assembly from Oxford Nanopore or PacBio long reads using Flye and Canu. Produces highly contiguous assemblies suitable for complete bacterial genomes and resolving complex regions. Use when assembling genomes from ONT or PacBio reads. tool_type: cli primary_tool: Flye measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Ass...Votes: 0GitHub stars: 6
- Metagenome Assembly--> --- name: bio-genome-assembly-metagenome-assembly description: Metagenome assembly from long reads using metaFlye and metaSPAdes with binning strategies. Use when reconstructing genomes from microbial communities, recovering metagenome-assembled genomes (MAGs), or resolving strain-level variation in complex samples. tool_type: cli primary_tool: metaFlye measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_comma...Votes: 0GitHub stars: 6
- Scaffolding--> --- name: bio-genome-assembly-scaffolding description: Scaffold contigs into chromosome-level assemblies using Hi-C data with YaHS, 3D-DNA, SALSA2, and validate with BUSCO and contact maps. Use when scaffolding contigs to chromosome-level assemblies. tool_type: cli primary_tool: YaHS measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Short Read Assembly--> --- name: bio-genome-assembly-short-read-assembly description: De novo genome assembly from Illumina short reads using SPAdes. Covers bacterial, fungal, and small eukaryotic genome assembly, as well as metagenome and transcriptome assembly modes. Use when assembling genomes from Illumina reads. tool_type: cli primary_tool: SPAdes measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Assemble genomes ...Votes: 0GitHub stars: 6
- Base Editing Design--> --- name: bio-genome-engineering-base-editing-design description: Design guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. Select optimal positions for C-to-T or A-to-G conversions without double-strand breaks. Use when designing base editor experiments for precise nucleotide changes. tool_type: python primary_tool: BE-Hive measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools...Votes: 0GitHub stars: 6
- Grna Design--> --- name: bio-genome-engineering-grna-design description: Design guide RNAs for CRISPR-Cas9/Cas12a experiments using CRISPRscan and local scoring algorithms. Score guides for on-target activity using Rule Set 2 and Azimuth models. Use when designing sgRNAs for gene knockout, activation, or repression experiments. tool_type: python primary_tool: crisprscan measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_com...Votes: 0GitHub stars: 6
- Hdr Template Design--> --- name: bio-genome-engineering-hdr-template-design description: Design homology-directed repair donor templates for CRISPR knock-ins using primer3-py. Create ssODN, dsDNA, or plasmid templates with optimized homology arms. Use when designing donor templates for precise insertions, tagging, or allele replacement. tool_type: python primary_tool: primer3-py measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_co...Votes: 0GitHub stars: 6
- Off Target Prediction--> --- name: bio-genome-engineering-off-target-prediction description: Predict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. Identify potential unintended cleavage sites genome-wide and assess guide specificity. Use when evaluating guide RNA specificity or selecting guides with minimal off-target risk. tool_type: cli primary_tool: Cas-OFFinder measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run...Votes: 0GitHub stars: 6
- Prime Editing Design--> --- name: bio-genome-engineering-prime-editing-design description: Design pegRNAs for prime editing using PrimeDesign algorithms. Generate spacer, PBS, and RT template sequences for precise genomic modifications without double-strand breaks. Use when designing prime editing experiments for precise insertions, deletions, or point mutations. tool_type: python primary_tool: PrimeDesign measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:...Votes: 0GitHub stars: 6
- Bed File Basics--> --- name: bio-genome-intervals-bed-file-basics description: BED file format fundamentals, creation, validation, and basic operations. Covers BED3 through BED12 formats, coordinate systems, sorting, and format conversion using bedtools and pybedtools. Use when working with genomic coordinates or preparing interval files for downstream tools. tool_type: mixed primary_tool: bedtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - ...Votes: 0GitHub stars: 6
- Bedgraph Handling--> --- name: bio-bedgraph-handling description: Create, manipulate, and convert bedGraph files for genome browser visualization. Covers bedGraph format, conversion to/from bigWig, normalization, and signal processing. Use when handling coverage and signal tracks from ChIP-seq, ATAC-seq, or RNA-seq. tool_type: mixed primary_tool: pyBigWig measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- bedGraph is ...Votes: 0GitHub stars: 6
- Bigwig Tracks--> --- name: bio-genome-intervals-bigwig-tracks description: Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC tools and pyBigWig. Use when preparing coverage tracks for genome browsers or extracting signal at specific regions. tool_type: mixed primary_tool: pyBigWig measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: ...Votes: 0GitHub stars: 6
- Coverage Analysis--> --- name: bio-genome-intervals-coverage-analysis description: Calculate read depth and coverage across genomic intervals using bedtools genomecov and coverage. Generate bedGraph files, compute per-base depth, and summarize coverage statistics. Use when assessing sequencing depth, creating coverage tracks, or evaluating target capture efficiency. tool_type: mixed primary_tool: bedtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tool...Votes: 0GitHub stars: 6
- Gtf Gff Handling--> --- name: bio-genome-intervals-gtf-gff-handling description: Parse, query, and convert GTF and GFF3 annotation files. Extract gene, transcript, and exon coordinates using gffread, gtfparse, and gffutils. Use when extracting specific features from gene annotations or converting between annotation formats. tool_type: mixed primary_tool: gffread measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- GTF ...Votes: 0GitHub stars: 6
- Interval Arithmetic--> --- name: bio-genome-intervals-interval-arithmetic description: Core interval arithmetic operations including intersect, subtract, merge, complement, map, and groupby using bedtools and pybedtools. Use when finding overlapping regions, removing overlaps, combining adjacent intervals, or transferring annotations between interval files. tool_type: mixed primary_tool: bedtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_f...Votes: 0GitHub stars: 6
- Proximity Operations--> --- name: bio-genome-intervals-proximity-operations description: Find nearest features, search within windows, and extend intervals using closest, window, flank, and slop operations. Use when performing TSS proximity analysis, assigning enhancers to genes, defining promoter regions, or finding nearby genomic features. tool_type: mixed primary_tool: bedtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_c...Votes: 0GitHub stars: 6
- Basecalling--> --- name: bio-basecalling description: Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Note: Guppy is deprecated; use Dorado for all new analyses. tool_type: cli primary_tool: dorado measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_fi...Votes: 0GitHub stars: 6
- Clair3 Variants--> --- name: bio-long-read-sequencing-clair3-variants description: Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels. Use when calling germline variants from ONT or PacBio alignments, particularly when high accuracy is needed for clinical or research applications. tool_type: cli primary_tool: Clair3 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Isoseq Analysis--> --- name: bio-long-read-sequencing-isoseq-analysis description: Analyze PacBio Iso-Seq data for full-length isoform discovery and quantification. Use when characterizing transcript diversity or identifying novel splice variants. tool_type: cli primary_tool: IsoSeq3 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Long Read Alignment--> --- name: bio-longread-alignment description: Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use when aligning ONT or PacBio reads to a reference genome for variant calling, SV detection, or coverage analysis. tool_type: cli primary_tool: minimap2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6
- Long Read Qc--> --- name: bio-longread-qc description: Quality control for long-read sequencing data using NanoPlot, NanoStat, and chopper. Generate QC reports, filter reads by length and quality, and visualize read characteristics. Use when assessing ONT or PacBio run quality or filtering reads before assembly or alignment. tool_type: cli primary_tool: nanoplot measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 6