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Getting Started

Get running with Krewlyzer in 5 minutes.

Quick Install

docker pull ghcr.io/msk-access/krewlyzer:0.5.2

git clone https://github.com/msk-access/krewlyzer.git && cd krewlyzer
git lfs pull && pip install -e .

pip install krewlyzer
git clone --depth 1 https://github.com/msk-access/krewlyzer.git ~/.krewlyzer-data
cd ~/.krewlyzer-data && git lfs pull
export KREWLYZER_DATA_DIR=~/.krewlyzer-data/src/krewlyzer/data

pip Users

See Installation Guide for KREWLYZER_DATA_DIR setup.

Your First Analysis

Run all fragmentomics features on a BAM file:

krewlyzer run-all sample.bam \
    --reference hg19.fa \
    --output results/

Check Results

ls results/
# sample.bed.gz            # Extracted fragments
# sample.EndMotif.tsv      # End motif frequencies
# sample.FSC.tsv           # Fragment size coverage
# sample.FSR.tsv           # Fragment size ratios
# sample.FSD.tsv           # Size distribution by arm
# sample.WPS.tsv.gz        # Windowed protection scores
# sample.OCF.tsv           # Orientation-aware fragmentation

Common Workflows

Targeted Panel (MSK-ACCESS)

For MSK-ACCESS v1 or v2 panels, use the --assay flag for panel-optimized analysis:

krewlyzer run-all sample.bam \
    --reference hg19.fa \
    --output results/ \
    --assay xs2 \
    --target-regions MSK-ACCESS-v2_targets.bed

This enables: - Gene-level FSC aggregation (146 genes) - Dual WPS output (genome-wide + panel-specific) - On/off-target splitting for all features

For PON normalization: 

krewlyzer run-all sample.bam \
    --reference hg19.fa \
    --output results/ \
    --assay xs2 \
    --target-regions targets.bed \
    --pon-model xs2.pon.parquet \
    --generate-json

→ Full MSK-ACCESS Quickstart for detailed workflows.

With Variant Analysis

Add mutant fragment size analysis using a VCF/MAF:

krewlyzer run-all sample.bam \
    --reference hg19.fa \
    --output results/ \
    --variants variants.maf

Individual Tools

Run specific features separately:

# Extract fragments first
krewlyzer extract -i sample.bam -r hg19.fa -o output/

# Then run feature tools on the BED
krewlyzer fsc -i output/sample.bed.gz -o output/
krewlyzer wps -i output/sample.bed.gz -o output/

Next Steps