Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for more accurate estimates.
Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers.
Query decomposition and multi-source search orchestration. Breaks natural language questions into targeted searches per source, translates queries into source-specific syntax,…
Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations.
Combines search results from multiple sources into coherent, deduplicated answers with source attribution.
Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing…
Create publication-quality plots and visualizations using matplotlib and seaborn. Works with ANY LLM provider (GPT, Gemini, Claude, etc.).
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…
Select and configure linear solvers for Ax=b systems arising in numerical simulations — choose between direct (LU, Cholesky) and iterative (CG, GMRES, BiCGSTAB, MINRES) methods,…
Handle mental health crisis situations in AI coaching safely. Use when implementing crisis detection, safety protocols, emergency escalation, or suicide prevention features.
Select and configure time integration methods for ODE and PDE simulations — choose among explicit Runge-Kutta, BDF, Rosenbrock, and Adams families, set relative and absolute error…
Validate material sample annotations against ontology constraints — check that class names and property names exist in the ontology, verify domain and range consistency for object…
Detect crisis signals in user content using NLP, mental health sentiment analysis, and safe intervention protocols.