Workflow for read alignment, sorting, indexing, mapping statistics, and downstream-ready alignment artifacts.
日本語の概要は準備中です。原文の説明を表示しています。
BioTender-max/awesome-bio-agent-skills2012026年7月2日 更新
無料GitHub で公開
bio-reporting-automated-qc-reports
Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC. Use when summarizing QC metrics across samples, creating shareable quality reports, or building automated QC pipelines.
含まれるファイル（3）
- SKILL.md2.6 KB
- examples/multiqc_pipeline.sh3.6 KB
- usage-guide.md1.5 KB
SKILL.md（原文）
インストールする前に、エージェントに与えられる指示の中身を確認できます。
Version Compatibility
Reference examples tested with: Cell Ranger 8.0+, FastQC 0.12+, GATK 4.5+, HISAT2 2.2.1+, MultiQC 1.21+, STAR 2.7.11+, Subread 2.0+, bcftools 1.19+, fastp 0.23+, kallisto 0.50+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Automated QC Reports with MultiQC
"Aggregate QC results into one report" → Combine outputs from FastQC, samtools, Picard, and other tools into a single interactive HTML report.
- CLI:
multiqc .(scans current directory for recognized tool outputs)
Basic Usage
# Aggregate all QC outputs in directory
multiqc results/ -o qc_report/
# Specify output name
multiqc results/ -n my_project_qc
# Include specific tools only
multiqc results/ --module fastqc --module star
Supported Tools
MultiQC recognizes outputs from 100+ bioinformatics tools:
| Category | Tools |
|---|---|
| Read QC | FastQC, fastp, Cutadapt |
| Alignment | STAR, HISAT2, BWA, Bowtie2 |
| Quantification | featureCounts, Salmon, kallisto |
| Variant Calling | bcftools, GATK |
| Single-cell | CellRanger, STARsolo |
Configuration
Create multiqc_config.yaml:
title: "RNA-seq QC Report"
subtitle: "Project XYZ"
intro_text: "QC metrics for all samples"
# Custom sample name cleaning
extra_fn_clean_exts:
- '.sorted'
- '.dedup'
# Report sections to include
module_order:
- fastqc
- star
- featurecounts
# Highlight samples
table_cond_formatting_rules:
pct_mapped:
fail: [{lt: 50}]
warn: [{lt: 70}]
Custom Data
# Add custom data file
# File format: sample\tmetric1\tmetric2
multiqc results/ --data-format tsv --custom-data-file custom_metrics.tsv
Python API
from multiqc import run as multiqc_run
# Run programmatically
multiqc_run(analysis_dir='results/', outdir='qc_report/')
Related Skills
- read-qc/quality-reports - Generate input FastQC reports
- read-qc/fastp-workflow - Preprocessing QC
- workflows/rnaseq-to-de - Full workflow with QC
レビュー
まだレビューはありません。使ってみた感想をお寄せください。
同じリポジトリのスキル
概要と使いどころ
Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.
日本語の概要は準備中です。原文の説明を表示しています。
BioTender-max/awesome-bio-agent-skills2012026年7月2日 更新
AlphaFold2 / AlphaFold-Multimer structure prediction for validation and confidence scoring. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm2-sequence-scoring. For QC thresholds, use protein-design-qc.
日本語の概要は準備中です。原文の説明を表示しています。
BioTender-max/awesome-bio-agent-skills2012026年7月2日 更新
Workflow for event-level and isoform-level splicing analysis with sashimi-ready outputs and splice QC.
日本語の概要は準備中です。原文の説明を表示しています。
BioTender-max/awesome-bio-agent-skills2012026年7月2日 更新
atac-seq
無料ATAC-seq processing with assay QC, MACS3 peak calling, consensus peak matrices, differential accessibility, and motif or footprint follow-up.
日本語の概要は準備中です。原文の説明を表示しています。
BioTender-max/awesome-bio-agent-skills2012026年7月2日 更新
End-to-end binder design using BindCraft hallucination. Use this skill when: (1) Designing protein binders with built-in AF2 validation, (2) Running production-quality binder campaigns, (3) Using different design protocols (fast, default, slow), (4) Need joint backbone and sequence optimization, (5) Want high experimental success rate. For backbone-only generation, use rfdiffusion. For QC thresholds, use protein-qc. For tool selection guidance, use binder-design.
日本語の概要は準備中です。原文の説明を表示しています。
BioTender-max/awesome-bio-agent-skills2012026年7月2日 更新