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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 49 of 545 min read

Module 43: Benchmarking

43.1 What to Benchmark, and Why It's Not Just "How Long Did It Take" Pipeline benchmarking spans several distinct, sometimes competing dimensions: Wall clock time — total elapsed time for a run, the most visible metric…

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