archive:computer_resources:assemblies
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archive:computer_resources:assemblies [2011/05/31 20:28] karplus [slug/] More on mitochondrial genome |
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 1.05 - can handle gzipped fastq files. | ||
| + | * Runs with k27, 31, 47, and 63 so far. 47 was the best overall. 63 got the longest contig (~14.9kb). | ||
| + | * Run parameters: | ||
| + | - pregraph: | ||
| + | * lowest count size of 2 (-d 2) | ||
| + | - contig: | ||
| + | * solve tiny repeats on (-R) | ||
| + | - map: | ||
| + | * all default | ||
| + | - scaff: | ||
| + | * intra-scaffold gap closure on (-F) | ||
archive/computer_resources/assemblies.txt · Last modified: 2015/09/02 16:53 by 92.247.181.31
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