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 [2011/06/02 19:26] eyliaw |
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| * 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. | * 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. | ||
| + | * 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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