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deeptools - NGS data analysis with deepTools

Processes sequencing alignments, performs quality control and normalization, compares samples, and generates genomic signal visualizations.

Tags

Updated: 2026-10-04
NGS analysisChIP-seqRNA-seqATAC-seqquality controlgenomic visualization

Capabilities

Convert BAM to coverage tracksValidate BAM, BED, and bigWigAssess sequencing qualityCompare and correlate samples

Typical Inputs

BAM alignment filesBAM index filesBED region files

Typical Outputs

bigWig coverage tracksbedGraph coverage tracksQuality control reports

What this skill does

  • Convert BAM to coverage tracks
  • Validate BAM, BED, and bigWig
  • Assess sequencing quality
  • Compare and correlate samples
  • Generate heatmaps and profiles
  • Analyze enrichment and peaks

Inputs

  • BAM alignment files
  • BAM index files
  • BED region files
  • bigWig signal files
  • Reference genome information
  • Analysis parameters

Outputs

  • bigWig coverage tracks
  • bedGraph coverage tracks
  • Quality control reports
  • Correlation and PCA results
  • Heatmaps and profile plots
  • Workflow scripts

Requirements

  • Python 3.12 or later
  • deepTools 4.0.0
  • pysam and pyBigWig
  • samtools for sorting and indexing workflows

Source

  • Spec: SKILL.md

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