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Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacterial, viral, adapter, or sample swap contamination. Use when suspecting cross-contamination or working with samples prone to microbial contamination.
Guide for writing SELECT, INSERT, UPDATE, DELETE queries with workers-qb
Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.
Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter content, GC bias, duplication levels, and overrepresented sequences. Use when performing initial QC on raw sequencing data or validating preprocessing results.
Sequencing quality control skill for assessing read quality, adapter contamination, and sequence composition
All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation. Use when preprocessing Illumina data and wanting a single fast tool instead of separate Cutadapt, Trimmomatic, and FastQC steps.
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships. Use when assessing count matrix quality before DE analysis.
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.
MaxQuant mass spectrometry skill for protein identification and quantification
Advanced Python unit testing framework for customer support tech enablement, covering FastAPI, SQLAlchemy, PostgreSQL, async operations, mocking, fixtures, parametrization, coverage, and comprehensive testing strategies for backend support systems
Local-only CockroachDB 성능 점검 자동화 스킬. 로컬 CockroachDB 단일 노드를 띄우고(선택), 프로젝트 DDL을 로컬 DB에 적용한 뒤(seed SQL 실행 포함), 실행된 쿼리(Statement Statistics)와 선택된 쿼리의 EXPLAIN ANALYZE를 기반으로 성능 진단을 수행한다. 결과는 “개선 필요 항목 + 개선 방안”이 포함된 CSV로 출력한다. 원격/클라우드 DB 연결 문자열이면 즉시 실패해야 한다(로컬 DB만 허용).
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.
Local search/indexing CLI (BM25 + vectors + rerank) with MCP mode.
RNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverage, and transcript integrity metrics. Use when validating RNA-seq libraries before differential expression analysis.
QBot项目模块开发的接口规范、最佳实践和开发指南。所有新模块必须遵循此规范。
Remove 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.
综合分子生物学工具包。用于序列操作、文件解析(FASTA/GenBank/PDB)、系统发育学和程序化NCBI/PubMed访问(Bio.Entrez)。最适合批处理、定制生物信息学管道、BLAST自动化。快速查找请使用gget；多服务集成请使用bioservices。
Post-training 4-bit quantization for LLMs with minimal accuracy loss. Use for deploying large models (70B, 405B) on consumer GPUs, when you need 4× memory reduction with <2% perplexity degradation, or for faster inference (3-4× speedup) vs FP16. Integrates with transformers and PEFT for QLoRA fine-tuning.
Quarantines or disables flaky/problematic tests using the QuarantineTools utility
Comprehensive guide for writing tests in magenta.nvim, including test environment setup, mock providers, driver interactions, and best practices
