MarkDup

A fast, accurate BAM deduplication tool with intelligent UMI detection and correct fragment detection.

Why MarkDup?

MarkDup solves critical issues in BAM deduplication:

Correct fragment detection: Proper strand-aware coordinate handling.
High performance: Optimized algorithms and parallel processing.
Smart UMI clustering: Frequency-aware algorithms to prevent over-merging.
Automatic detection: Handles both UMI and non-UMI data seamlessly.

Quick Start

# Installation
pip install markdup

# Basic usage (auto-detects everything)
markdup -i input.bam -o output.bam

# With multiple threads
markdup -i input.bam -o output.bam --threads 8

# Force coordinate-based (no UMIs)
markdup -i input.bam -o output.bam --no-umi

Usage

For a full list of options and their descriptions, run:

markdup --help

Examples

Basic Deduplication

# Auto-detect UMIs and process
markdup -i input.bam -o output.bam

# Force coordinate-based method (no UMIs)
markdup -i input.bam -o output.bam --no-umi

Advanced Options

# Custom UMI settings
markdup -i input.bam -o output.bam --umi-tag UB --max-dist-frac 0.15

# Start-only positioning (useful for ChIP-seq)
markdup -i input.bam -o output.bam --start-only

# Keep duplicates and mark them
markdup -i input.bam -o output.bam --keep-duplicates

Output Format

MarkDup adds BAM tags to track deduplication:

Tag	Description
`cn`	Cluster name (chr:start-end:strand:UMI)
`cs`	Cluster size (number of reads)

Documentation

License

MIT License - see LICENSE for details.

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