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archive:computer_resources:assemblies [2011/06/02 19:27] eyliaw [slug/] |
archive:computer_resources:assemblies [2011/06/03 15:40] karplus [slug/] added more on mitochondrion assembly |
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- assemble them using SOAPdenovo. | - assemble them using SOAPdenovo. | ||
* It looks like the Illumina reads have about 228x coverage of the mitochondrion, but coverage is patchy, and it seems to be difficult to close the circle (at least with SOAPdenovo). | * It looks like the Illumina reads have about 228x coverage of the mitochondrion, but coverage is patchy, and it seems to be difficult to close the circle (at least with SOAPdenovo). | ||
- | * I have an almost complete mitochondrial genome, and I'm hoping that a few more iterations or some tricky assembly will close it into a clean circular genome. | + | * We have an almost complete mitochondrial genome, and I'm hoping that a few more iterations or some tricky assembly will close it into a clean circular genome. |
+ | * It turns out that a lot of the hard hand work and iterated searching to assemble the mitochondrion was not necessary, as the SOAPdenovo-assembly2/k63_w_454_contigs/ assembly now has a 14960-long contig (not scaffold!) which is an almost-full-length mitochondrion, roughly as good as the best I've managed to assemble so far. I'll combine it with my efforts and see if I can eke out a few more bases. | ||
* SOAPdenovo-assembly2/ Assembly with new + old Illumina and 454 data. | * SOAPdenovo-assembly2/ Assembly with new + old Illumina and 454 data. | ||
* SOAPdenovo 1.05 - can handle gzipped fastq files. | * SOAPdenovo 1.05 - can handle gzipped fastq files. |