genomics-alignment

name	genomics-alignment
description	Alignment statistics from SAM/BAM files: mapping rate, MAPQ distribution, insert size, duplicate rate, proper pair rate. Mirrors samtools-flagstat.
version	0.2.0
author	OmicsClaw
license	MIT
tags	["genomics","alignment","BWA","Bowtie2","Minimap2"]
metadata	{"omicsclaw":{"domain":"genomics","emoji":"🎯","trigger_keywords":["alignment","BWA","Bowtie2","Minimap2","map reads"],"allowed_extra_flags":["--method"],"legacy_aliases":["align"],"saves_h5ad":false}}

🎯 Genomics Read Alignment

Short and long read alignment to reference genomes. Supports BWA-MEM, Bowtie2, and Minimap2.

CLI Reference

python omicsclaw.py run genomics-alignment --demo
python omicsclaw.py run genomics-alignment --input <reads.fastq> --output <dir>

Why This Exists

• Without it: Alignment is run with disparate tools and ad-hoc flags causing unrecoverable errors downstream
• With it: Unified syntax automatically scaling threads and standardizing BAM/CRAM outputs
• Why OmicsClaw: Provides a standard local-first interface with built-in QC logging.

Workflow

1. Calculate: Prepare sequences and parameterize indexing.
2. Execute: Run primary alignment heuristics over genomes.
3. Assess: Perform mapping quality filtering and deduplication.
4. Generate: Output structural mappings or sorted BAMs.
5. Report: Synthesize alignment stats into tables.

Example Queries

• "Run alignment on my fastq data using BWA"
• "Map long reads using Minimap2 to reference"

Output Structure

output_directory/
├── report.md
├── result.json
├── processed.bam
├── figures/
│   └── mapping_stats.png
├── tables/
│   └── alignment_metrics.csv
└── reproducibility/
    ├── commands.sh
    ├── requirements.txt
    └── checksums.sha256

Safety

• Local-first: Strict offline processing without external upload.
• Disclaimer: Requires OmicsClaw reporting structures and disclaimers.
• Audit trail: Hyperparameters and operational flow states are logged fully.

Integration with Orchestrator

Trigger conditions:

• Automatically invoked dynamically based on tool metadata and user intent matching.

Chaining partners:

• genomics-qc — Upstream quality checks
• variant-call — Downstream variant discovery

Citations

• BWA-MEM
• Minimap2