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lecture_notes:04-13-2011 [2011/04/15 19:15]
eyliaw [De Bruijn Graphs]
lecture_notes:04-13-2011 [2011/04/15 19:22]
eyliaw [De Bruijn Graphs]
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 Specifically,​ the de Bruijn graph breaks each read into words and paths through the words, mapping new reads to form a graph structure. ​ Velvet then simplifies this graph by removing unjoined tips and reducing parallel strands into the strand with the maximum coverage (this error corrects for mismatched bases). ​ Velvet leaves loops unresolved in the final structure, as these represent repeat regions. [(cite:​Velvet>​Zerbino,​ D. and Birney, E. Specifically,​ the de Bruijn graph breaks each read into words and paths through the words, mapping new reads to form a graph structure. ​ Velvet then simplifies this graph by removing unjoined tips and reducing parallel strands into the strand with the maximum coverage (this error corrects for mismatched bases). ​ Velvet leaves loops unresolved in the final structure, as these represent repeat regions. [(cite:​Velvet>​Zerbino,​ D. and Birney, E.
-Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008. 18: 821-829. doi: 10.1101/​gr.074492.107)]+Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008. 18: 821-829. doi: [[http://​dx.doi.org/​10.1101/​gr.074492.107|10.1101/​gr.074492.107]])] 
 +===== Extensions ===== 
 +==== Shorty ==== 
 +Shorty uses the variance in paired read lengths to build larger contigs from small ones.  It bears some resemblence to how [[bioinformatic_tools:​PRICE|PRICE]] does contig extension. 
 +==== Oasis ==== 
 +Oasis does splicing analysis on words with more than one connection, breaking them up into separate contigs. ​ This resolves nodes in the de Bruijn graph. 
 +==== Columbus ==== 
 +Columbus is a combined approach between mapping and de novo sequencing. ​ It uses a reference sequence to organize contigs, but allows for novel structures within the contigs.
lecture_notes/04-13-2011.txt · Last modified: 2015/08/20 09:46 by 217.73.208.146