lecture_notes:04-13-2011
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
|
lecture_notes:04-13-2011 [2011/04/15 19:13] eyliaw |
lecture_notes:04-13-2011 [2011/04/15 19:16] eyliaw [De Bruijn Graphs] |
||
|---|---|---|---|
| Line 1: | Line 1: | ||
| ====== Velvet, Dan Zerbino ====== | ====== Velvet, Dan Zerbino ====== | ||
| ===== De Bruijn Graphs ===== | ===== De Bruijn Graphs ===== | ||
| - | Velvet uses de Bruijn graphs to condense reads and resolve common sequencing problems. Compared to overlap layout consensus, it simplifies multiple reads by resolving repeats into only one node, so that their counts only need to be stored on top. This reduces the amount of memory required to store the reads by the dimension of coverage. | + | [[bioinformatic_tools:velvet|Velvet]] uses de Bruijn graphs to condense reads and resolve common sequencing problems. Compared to overlap layout consensus, it simplifies multiple reads by resolving repeats into only one node, so that their counts only need to be stored on top. This reduces the amount of memory required to store the reads by the dimension of coverage. |
| 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]])] |
lecture_notes/04-13-2011.txt · Last modified: 2015/08/20 09:46 by 217.73.208.146
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Noncommercial-Share Alike 3.0 Unported
