# Banana Slug Genomics

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lecture_notes:04-15-2015

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 lecture_notes:04-15-2015 [2015/04/15 14:05]chkcole created lecture_notes:04-15-2015 [2015/04/15 15:31]chkcole 2015/04/17 10:38 almussel 2015/04/15 15:31 chkcole 2015/04/15 15:31 chkcole 2015/04/15 14:05 chkcole 2015/04/15 14:05 chkcole created Next revision Previous revision 2015/04/17 10:38 almussel 2015/04/15 15:31 chkcole 2015/04/15 15:31 chkcole 2015/04/15 14:05 chkcole 2015/04/15 14:05 chkcole created Next revision Both sides next revision Line 7: Line 7: 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. + + 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 kmer can be extended into another kmer.