lecture_notes:04-15-2015

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The rate-limiting step for this process is calculating the overlap between each sequence because the process time increases exponentially with the number of sequences in the data set. | The rate-limiting step for this process is calculating the overlap between each sequence because the process time increases exponentially with the number of sequences in the data set. | ||

- | Assembling genomes with a De Bruijn graph circumvents this problem by allowing the assembler to extend the genome independently of any other sequence in the data. In order to assemble the genome with a De Bruijn graph, you must select a k-mer size such that the genome being assembled contains few or no repeats when divided into k-mers of that size. | + | Assembling genomes with a De Bruijn graph circumvents this problem by allowing the assembler to extend the genome independently of any other sequence. In order to assemble the genome with a De Bruijn graph, you must select a k-mer size such that the genome being assembled contains few or no repeats when divided into k-mers of that size. |

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+ | The graph is built by dividing each sequence into k-mers of a given length and constructing nodes such that each node contains a k-mer, and a directed edge from one node to another means that one k-mer can be extended into another k-mer. |

lecture_notes/04-15-2015.txt · Last modified: 2015/04/17 10:38 by almussel