Genome assembly

Question 1

FASTQ

Answer 1

Four line of sequence, line 1 starts with @, line 3 starts with +, line 4 encodes the quality values.

Question 2

FASTA file

Answer 2

A FASTA file contains sequence information readable by many programs.

Question 3

Genome assembly

Answer 3

Programs combine fragmented DNA reads to construct the genome, ideally using long, high-quality reads to manage the complexity.

Question 4

Contig structure

Answer 4

Contiguous sequence formed by several overlapping reads without any gaps.

Question 5

A scaffold in genome assembly

Answer 5

Ordered and oriented set of contigs.

Question 6

N50 statistic

Answer 6

Weighted median statistic where 50% of the total assembly length is contained in contigs or scaffolds of length N or larger.

Question 7

De novo vs comparative genome assembly

Answer 7

Involves assembling reads to form a new sequence without a reference genome, whereas comparative assembly aligns reads against an existing reference sequence.

Question 8

De Bruijn graph

Answer 8

Graph representing overlaps between sequences of symbols, used in genome assembly by splitting reads into uniform sized units.

Question 9

Eulerian walk in a graph

Answer 9

Closed trail in a graph with no repeated edges covering all edges of the graph.