> ## Documentation Index
> Fetch the complete documentation index at: https://docs.biomni.phylo.bio/llms.txt
> Use this file to discover all available pages before exploring further.

# Workflow Templates

> Use pre-built analysis workflows to accelerate your research

Workflow templates are pre-built analysis pipelines curated by the Biomni Lab team. They help you get started quickly with common bioinformatics tasks.

## Using a Template

### From the Chat Input

Click the **+ Workflow** button in the chat input area to browse available templates:

1. Click **+ Workflow** next to the chat input
2. Browse templates by category or search
3. Click a template to see its description and requirements
4. Click **Use Template** to apply it
5. Provide the required input files when prompted

### From Suggested Templates

When you start a new task, relevant workflow templates appear in the chat area based on common use cases:

1. Click on a template to see what it does
2. Click **Use Template** to apply it
3. Provide the required input files when prompted

## Template Examples

### RNA-seq Differential Expression

Performs full RNA-seq analysis from raw reads:

1. Quality control with FastQC
2. Alignment with STAR
3. Quantification with featureCounts
4. Differential expression with DESeq2
5. Visualization with volcano plots and heatmaps

**Required inputs**: Paired-end FASTQ files, sample metadata

### Single-cell Clustering

Analyzes single-cell RNA-seq data:

1. Quality filtering
2. Normalization and scaling
3. Dimensionality reduction (PCA, UMAP)
4. Clustering
5. Marker gene identification

**Required inputs**: Count matrix or 10x Genomics output

### Variant Calling

Identifies genetic variants from sequencing data:

1. Alignment to reference genome
2. Mark duplicates
3. Base quality recalibration
4. Call variants with GATK
5. Variant annotation with VEP

**Required inputs**: FASTQ files, reference genome