What is Assembly and annotation?

Assembly reconstructs a genome from its reads by overlap: in an overlap graph each read is a node joined to the reads it overlaps; in a de Bruijn graph, used for billions of short reads, every $k$-mer (subsequence of length $k$) is a node and the genome is a path through them. Both are broken by repeats longer than the read, which give branching paths. Contigs are ordered and oriented into scaffolds by paired-end reads and long-range information (long reads, optical maps, chromosome-contact maps), and the scaffolds are placed on chromosomes. Assembly quality is summarised by the N50: the contig length such that half of the assembled bases lie in contigs at least that long. Annotation then finds the genes: in bacteria, open reading frames longer than chance; in eukaryotes, by combining sequence signals (splice sites, promoters, codon bias), homology to known proteins, and transcripts sequenced from RNA. The result, for a species, is a reference genome to which every later read from that species is aligned rather than assembled anew.