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A Nextflow DSL2 pipeline for separating human and mouse sequencing reads from Patient-Derived Xenograft (PDX) samples using [Xengsort](https://gitlab.com/genomeinformatics/xengsort) (Zentgraf and Rahmann, 2021).
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## Workflow
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![Pipeline Workflow](pipeline.svg)
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## 🎯 Overview
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When tumor samples from PDX models (human tumors grown in immunocompromised mice) are sequenced, the resulting data contains a mixture of:
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- **Production-ready**: Docker and Singularity support for reproducibility
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- **NSG-optimized**: Compatible with NSG-adapted mouse reference genome
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## Workflow
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![Pipeline Workflow](pipeline.svg)
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## 🚀 Quick Start
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