archive:computer_resources:assemblies
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archive:computer_resources:assemblies [2010/06/12 02:14] mpcusack |
archive:computer_resources:assemblies [2011/06/03 15:40] karplus [slug/] added more on mitochondrion assembly |
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| * is not high. 21k max scaffold size. Estimated | * is not high. 21k max scaffold size. Estimated | ||
| * genome size is around 3G. The 4 steps are | * genome size is around 3G. The 4 steps are | ||
| - | * 1. pregraph (3.5 to 4.5 hours for 30 to 60 cpus) | + | - pregraph (3.5 to 4.5 hours for 30 to 60 cpus) |
| - | * 2. contig (1.3 hours) | + | - contig (1.3 hours) |
| - | * 3. map (0.6 hours with 60cpus) - paired ends | + | - map (0.6 hours with 60cpus) - paired ends |
| - | * 4. scaff (1 hour with 60cpus) | + | - scaff (1 hour with 60cpus) |
| + | * barcode-of-life/ attempt to assemble the mitochondrial genome, with particular emphasis on the gene for mitochondrial cytochrome c oxidase subunit I protein I (CO1), which is used for the "barcode of life". [[http://www.boldsystems.org/|BOLD (barcode of life database)]] | ||
| + | * Started with a search of SOAPdenovo-assembly1/k31/soapSlug.scafSeq for scaffolds that matched examples from other mollusks. | ||
| + | * 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. | ||
| + | * 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). | ||
| + | * 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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