How many de Bruijn sequences?

Each of the eight 3-digit sequences (corresponding to the eight vertices) appears exactly twice, and each of the sixteen 4-digit sequences (corresponding to the 16 edges) appears exactly once.

How do you make a de Bruijn graph?

A de Bruijn graph can be constructed for any sequence, short or long. The first step is to choose a k-mer size, and split the original sequence into its k-mer components. Then a directed graph is constructed by connecting pairs of k-mers with overlaps between the first k-1 nucleotides and the last k-1 nucleotides.

Why are de Bruijn graphs useful for genome assembly?

Finding an Eulerian cycle allows one to reconstruct the genome by forming an alignment in which each successive k-mer (from successive edges) is shifted by one position. This generates the same cyclic genome sequence without the computational strain of finding a Hamiltonian cycle.

How do you pronounce de Bruijn?

The word “bruijn” essentially means the colour brown – although modern spelling would be “bruin”. Here are the various ways I have heard it pronounced, some of them in successive talks at ISMB 2013 in the same session even: broon. broo-en, brewin’

What is a contig in genetics?

A contig–from the word “contiguous”–is a series of overlapping DNA sequences used to make a physical map that reconstructs the original DNA sequence of a chromosome or a region of a chromosome.

What is a de Bruijn graph and what is it used for?

In bioinformatics, De Bruijn graphs are used for de novo assembly of sequencing reads into a genome.

What does 30x coverage mean?

The concept of coverage is similar to megapixels in your camera. The number before the ‘x’ is the coverage (the average number of times your genome will be sequenced). For example, when you get 30x WGS, the ’30x’ means that your entire genome will be sequenced an average of 30 times.

What does contig mean?

A contig–from the word “contiguous”–is a series of overlapping DNA sequences used to make a physical map that reconstructs the original DNA sequence of a chromosome or a region of a chromosome. A contig can also refer to one of the DNA sequences used in making such a map.

What is node in de Bruijn graph?

In a de Bruijn graph, the nodes represent the distinct k-mers that occur in the reads and there exists an edge between the two nodes if there is a (k–1)-length overlap between the suffix and prefix of the corresponding k-mers, respectively.

What is 10X sequencing?

The 10X Genomics technology generates individually barcoded sequencing libraries for hundreds of thousands of nanoliter volume oil droplets using up to 1.7 million different barcodes. The 10X Genome sequencing data contain conventional shotgun sequencing data, after trimming off the first 26 bases of the forward read.

What is contig mapping?

A contig is the physical map, which results from putting together several little overlapping bits of DNA into a longer sequence. The contig is the physical map resulting from taking small pieces of DNA that overlap and putting them together into a longer sequence.