Building a CNV Analysis Pipeline from Your Own Whole-Genome Data
A practical walkthrough for calling and filtering copy number variants from a 30x whole-genome CRAM, with the limits of what each caller can see.
Tag: pipelines
5 posts
Building an NGS Bioinformatics Pipeline for Your Own Genome and Transcriptome
A step-by-step guide to processing your own whole-genome and RNA sequencing data, and to validating the pipeline against a truth set.
How to Build a Genome Analyzer You Trust
What a genome analyzer is at the file level, from FASTQ to CRAM to VCF, and how to measure your own error floor against GIAB.
Building a Genomics Pipeline for Your Own Whole Genome
A step-by-step guide from raw FASTQ to an annotated variant table on your own machine, covering alignment, calling, QC thresholds and annotation.
Building a Small RNA-Seq Analysis Pipeline You Can Audit
A step-by-step pipeline for small RNA sequencing data, from adapter chemistry and UMI handling through hierarchical annotation, isomiR-level quantification, and differential expression, with the biofluid-specific failure modes that break naive runs.