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lecture_notes:06-02-2010 [2010/06/05 17:48] jstjohn |
lecture_notes:06-02-2010 [2010/06/06 22:32] (current) galt more rationale |
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+ | ====== Sea Hare and Panda ====== | ||
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+ | Looking at recent successful de-novo assemblies can help inform future sequencing and assembly plans for the Banana Slug. | ||
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+ | ===== Sea Hare ===== | ||
+ | |||
+ | Sea Hare is interesting because it is a recent de-novo mollusc assembly using 454 mate-pairs. | ||
+ | |||
* Analyzing data from previously sequenced mollusk genomes | * Analyzing data from previously sequenced mollusk genomes | ||
* Broad institute /ftp/pub/assemblies/invertebrates/aplysia (seahare) | * Broad institute /ftp/pub/assemblies/invertebrates/aplysia (seahare) | ||
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* Estimate error after mapping. | * Estimate error after mapping. | ||
* These two measures should be correlated to each other. | * These two measures should be correlated to each other. | ||
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+ | ===== Panda ===== | ||
+ | |||
+ | Panda is interesting because it is a recent de-novo assembly of a large | ||
+ | genome of approximately the same size as banana slug (3Gb). It is also | ||
+ | done using SOAPdenovo which we were able to use to assemble our slug data. | ||
+ | Panda is also the only known large genome yet assembled de-novo using | ||
+ | only Illumina/Solexa reads. | ||
Panda Genome statistics | Panda Genome statistics |