🧬 A general pipeline for data processing of 3 letter sequencing methods.

• ✂️ Clean Reads with Built-in & Custom Options

  • Auto-detects & removes adapters.
  • Built-in support for multiple library preparation schemes
  • Supports your custom adapters.
  • Optional contamination reads removal.
  • Mask high abundant reads (rRNA, spike-in oligo, ...) before genome alignment.

• ⚡ Processes Single-End (SE) & Paired-End (PE) Sequencing Data Simultaneously

  • Handles both SE and PE reads.
  • Mixed SE and PE reads for one sample is also supported.
  • Use for various sequencing projects.

• ➕ Auto-Combines Data from Multiple Sequencing Runs

  • Joins data from multiple runs for one sample.
  • Creates a single, complete dataset.
  • Report the combine process in the final report.

• 🚀 Simplified, Fast & Resource-Efficient Processing

  • Turns complex steps into easy ones.
  • Built for speed.
  • Parameterized for efficiency.

• cutseq
• samtools
• hisat3n
• umicollapse
• markduplicates
• pbr
• python: 3.10+ (and dependencies below)
  • scipy: 1.12.0+
  • polar: 1.30.0+

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