Abstract

When you assemble a new genome, you get its full sequence in FASTA format, in the form of contigs, scaffolds, or even whole chromosomes if you are lucky. However genomes, in particular for eukaryote organisms, contain a varying but significant proportion of repeated elements all along the sequence. These elements belong to different classes, including:

About This Material

This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.

Questions this will address

• How to mask repeats in a genome?
• What is the difference between hard and soft-masking?

Learning Objectives

• Use Red and RepeatMasker to soft-mask a newly assembled genome