Tag: ngs

A technical account of exome sequencing: capture chemistry, coverage statistics, and the failure modes that decide between WES and WGS.

A step-by-step guide to processing your own whole-genome and RNA sequencing data, and to validating the pipeline against a truth set.

A step-by-step guide to turning raw FASTQ files from whole-genome and RNA sequencing into aligned, called, annotated, and validated results on your own hardware, with the specific tools, flags, and quality thresholds we use.

A working guide to the files a sequencer produces and what to do with them: FASTQ through alignment, variant calling, annotation, and RNA quantification, with the commands, parameters, and failure modes that matter.

A step-by-step guide to going from raw FASTQ files to an aligned CRAM, a benchmarked variant call set, an annotated shortlist, and an RNA-seq expression table, with the actual commands, parameters, and quality thresholds we use.