lecture_notes:06-02-2010
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lecture_notes:06-02-2010 [2010/06/02 22:15] hyjkim created |
lecture_notes:06-02-2010 [2010/06/05 17:48] jstjohn |
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| * Next slug to be sequenced should be photographed during dissection in order to identify the species. | * Next slug to be sequenced should be photographed during dissection in order to identify the species. | ||
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| + | good computational challange: | ||
| + | * Subdivide small reads into regions that they group into, then you can do local denovo assemblies on subsets of reads. This is done biologically with things like the BACs. | ||
| + | * Example, shorty: map reads to a contig, then map out to reads in other contigs, and then map back. It collects a bunch of reads that might belong together and can assemble these. | ||
| + | * Can use SOAPdenovo to get initial contigs. Then can map pieces onto contigs and gather reads togeather. Store contigs in memory, and stream out data to sub-assemblers. PHD level question, can we make an efficient parallel assembler out of this? How to stream through this and partition efficiently? How can we get efficient ways of dealing with all of this? | ||
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lecture_notes/06-02-2010.txt ยท Last modified: 2010/06/06 22:32 by galt
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