Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka).
Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers.
Detect contamination and assess genome quality using CheckM, CheckM2, GTDB-Tk, and GUNC for metagenome-assembled genomes and isolate assemblies.
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…
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…
Metagenome assembly from long reads using metaFlye and metaSPAdes with binning strategies. Use when reconstructing genomes from microbial communities, recovering…
Scaffold contigs into chromosome-level assemblies using Hi-C data with YaHS, 3D-DNA, SALSA2, and validate with BUSCO and contact maps.
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…
BED file format fundamentals, creation, validation, and basic operations. Covers BED3 through BED12 formats, coordinate systems, sorting, and format conversion using bedtools and…
Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC — from…
Calculate read depth and coverage across genomic intervals using bedtools genomecov and coverage. Generate bedGraph files, compute per-base depth, and summarize coverage…
Parse, query, and convert GTF and GFF3 annotation files. Extract gene, transcript, and exon coordinates using gffread, gtfparse, and gffutils.
Core interval arithmetic operations including intersect, subtract, merge, complement, map, and groupby using bedtools and pybedtools.
Find nearest features, search within windows, and extend intervals using closest, window, flank, and slop operations.
Download, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels.
Calculate linkage disequilibrium statistics (r², D'), perform LD pruning for population structure analysis, identify haplotype blocks, and visualize LD patterns using PLI — from…
Python population genetics with scikit-allel. Read VCF files, compute allele frequencies, calculate diversity statistics, perform PCA, and run selection scans using Genot — from…
Detect signatures of natural selection using Fst, Tajima's D, iHS, XP-EHH, and other selection statistics.
Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations.
Design qPCR primers and TaqMan/molecular beacon probes using primer3-py. Configure probe Tm, primer-probe spacing, and hydrolysis probe constraints for real-time PCR assa — from…
Align 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. — from bg-szy/TOP-SKILLS
Creates reproducible Jupyter notebooks for bioinformatics analysis with parameterization using papermill.
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format.
Multi-omic biomarker discovery studio that ingests expression + metadata, performs QC, multi-strategy feature selection, nested CV model training, survival analysis hooks, and…
Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython.
Build tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints.
Perform flux balance analysis (FBA) and flux variability analysis (FVA) on genome-scale metabolic models using COBRApy.
Perform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions.
Build genome-scale metabolic models from genome sequences using CarveMe and gapseq for automated reconstruction. Generate draft models ready for curation and analysis.
Validate, gap-fill, and curate genome-scale metabolic models using memote for quality scores and COBRApy for manual curation.
Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications.
Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck.
Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution — from…
Create scalable, containerized bioinformatics pipelines with Nextflow DSL2 supporting Docker, Singularity, and cloud execution.
Build reproducible bioinformatics pipelines with Snakemake using rules, wildcards, and automatic dependency resolution.
Create portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution engines.
End-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and specialized editing strategies…
End-to-end CRISPR screen analysis from FASTQ to hit genes. Orchestrates guide counting, QC, statistical analysis with MAGeCK, and hit calling with multiple methods.
End-to-end flow cytometry workflow from FCS files to differential analysis. Orchestrates compensation, transformation, gating/clustering, and statistical testing with CAT — from…
End-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches.
End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and association testing for case-control or quantitative trait — from…
End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocessing, segmentation, phenotyping, and spatial statis — from…
End-to-end genome-scale metabolic modeling from genome sequence to flux predictions. Covers automated reconstruction with CarveMe, model validation with memote, FBA/FVA a — from…
End-to-end metabolomics workflow from raw MS data to pathway analysis. Orchestrates XCMS preprocessing, annotation, normalization, statistical analysis, and pathway mappi — from…
End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with M — from…
End-to-end TCR/BCR repertoire analysis from FASTQ to clonotype diversity metrics. Use when analyzing immune repertoire sequencing data from bulk or single-cell experiment — from…
Apply bioethical principles (autonomy, beneficence, non-maleficence, justice) and case-based reasoning to healthcare decisions, research protocols, and clinical dilemmas
Expert-level biology, biotechnology, genetics, bioinformatics, and computational biology
Use the local Biomni checkout to orchestrate its 150+ biomedical tools, databases, and know-how workflows for complex research questions.
Bluesky experimental orchestration skill for scan automation, data collection, and metadata management
Transform a product briefing into comprehensive, research-backed product management artifacts.
Amazon Braket integration skill for multi-vendor quantum hardware access and hybrid workflows
Research dispatcher for enhanced /build command Phase 1. Parses user concept input and delegates to claude-code-guide for capability inventory.
GLAW Investigations Bureau — Prosecutor Agent. The trial mind of the bench: case-theory construction, causes of action (civil + criminal), elements-to-evidence mapping, exposure…
BWA-MEM2 alignment skill for mapping sequencing reads to reference genomes with optimized parameter selection
CAMB cosmological perturbation skill for CMB power spectra, matter power spectra, and cosmological parameter estimation
Career Companion for frontier tech — AI, space, aerospace, robotics, drones, defense, autonomy. Searches live job openings, tailors resumes and CVs, runs mock interviews,…
GLAW Case-Law Research — the firm's affirmative precedent-hunter. Given a legal issue, it FINDS the controlling and persuasive authority (statutes, regulations, and cases on…
AI-powered analysis of cellular senescence for aging research, cancer therapy response, and senolytic drug development.
An LLM chemistry agent with expert-designed tools for organic synthesis, drug discovery, and materials design. — from bg-szy/TOP-SKILLS