Bienko and Crosetto labs - HT

🧬 In this repository we have all of the pipelines that are up-and-running for NGS analysis 👩‍🔬 🖥️

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Getting started using HPC

All of these pipelines have been modified so that they work on the HPC at the Human Technopole. There is lots of useful documentation for getting started on HPC on Service Now.
We have also written a couple of guides to help you get started:

1. Step-by-step guide for running jupyter lab on HPC: jupyter-step-by-step
2. How to install conda and create environments: conda-installation-guide

Available pipelines:

1. HiC using nextflow
2. BLISS ⚠️ work in progress!
3. scDNA-CNV using nextflow ⚠️ work in progress!
4. New Profiler 🌠 pipeline for radial profiling +/- deconwolf (from Giorgio, includes GUI!)