archive:computer_resources:assemblies
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archive:computer_resources:assemblies [2011/05/29 23:48] karplus [slug/] added barcode-of-life description |
archive:computer_resources:assemblies [2011/06/02 19:26] eyliaw |
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| * Looked for 454 reads that extended or joined contigs in scaffold | * Looked for 454 reads that extended or joined contigs in scaffold | ||
| * Repeated (sometimes using more sensitive searches) until no more credible scaffolds from the SOAPdenovo-assembly1/k31/ assembly nor 454 reads were found. | * Repeated (sometimes using more sensitive searches) until no more credible scaffolds from the SOAPdenovo-assembly1/k31/ assembly nor 454 reads were found. | ||
| - | * Next step (not done yet, as of 29 May 2011) is to find all Illumina reads that map to the mitochondrial draft and assemble them. | + | * The 454 coverage of the mitochondrion is so slight as to be nearly useless, so instead we can iterate: |
| + | - find all Illumina reads that map to the mitochondrial draft, using BWA | ||
| + | - 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). | ||
| + | * 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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