Working with a genome

Four pages, in the order a project usually needs them: get the reference onto this machine, read sequence out of it, attach an annotation, then build the index an aligner wants. Every one of them starts from Genome("<assembly>").

Page	What it answers
Assembly	How a reference is prepared, and what files that leaves on disk.
Sequences and regions	How to name a locus, and what a DNA object does for you.
Annotations	How a GTF is registered, and how to ask it which genes it carries.
Aligner indexes	How a STAR or chromap index is built, and how to find it again.

Transcription factors, motifs, gene identifiers and orthologs are keyed on a species rather than on an assembly. They are under Topics.