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ComputingLifeSci

A complete computational biology curriculum — 23 courses covering programming, databases, machine learning, genomics and research infrastructure. Written for biologists, not computer scientists.

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Nextflow & Snakemake54 chapters

Overview
Module 34: Building NGS Pipelines — General Principles
Module 35: RNA-seq Pipeline
Module 36: WGS Pipeline (Whole-Genome Sequencing — Alignment & Preprocessing)
Module 37: Variant Calling Pipeline (Germline)
Module 38: CNV Pipeline (Copy Number Variant Calling)
Module 39: Somatic Variant Calling Pipeline
Module 40: Fusion Pipeline (Gene Fusion Detection)
Module 41: Single-Cell Pipeline
Module 42: Multiomics Pipeline
Module 43: Benchmarking
Module 44: Best Practices
Module 45: CI/CD and GitHub Actions
Module 46: Real Datasets
Module 47: Complete Hands-On Capstone Projects
Course Conclusion

/Nextflow & Snakemake/Nextflow & Snakemake for Bioinformatics — Part 3 of 3

Chapter 47 of 546 min read

Module 41: Single-Cell Pipeline

41.1 Pipeline Goal and the Cell Barcode Aware Alignment Difference Single cell RNA seq (e.g., 10x Genomics Chromium data) requires demultiplexing reads by cell barcode and UMI (Unique Molecular Identifier) before/during…

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