archive:computer_resources:assemblies
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archive:computer_resources:assemblies [2010/06/12 02:14] mpcusack |
archive:computer_resources:assemblies [2011/05/29 23:48] karplus [slug/] added barcode-of-life description |
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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. | ||
| + | * 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. | ||
archive/computer_resources/assemblies.txt · Last modified: 2015/09/02 16:53 by 92.247.181.31
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