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archive:computer_resources:assemblies [2010/06/12 02:14] mpcusack |
archive:computer_resources:assemblies [2011/06/21 23:27] karplus [slug/] moved mitochondrion assembly information to a new page |
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* so ran with filling -R to get 12k maxcontig. | * so ran with filling -R to get 12k maxcontig. | ||
* Then ran the scaffolding steps with 200bp insert size. | * Then ran the scaffolding steps with 200bp insert size. | ||
- | * For all steps, used low default cutoffs since our 10x coverage | + | * For all steps, used low default cutoffs since our 10x coverage is not high. 21k max scaffold size. |
- | * is not high. 21k max scaffold size. Estimated | + | * Estimated genome size is around 3G. |
- | * genome size is around 3G. The 4 steps are | + | * 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, documented on its own page: [[computer_resources:assemblies:mitochondrion]] | ||
+ | * 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) | ||
+ | * Statistics for each kmer size assembly (using illumina and 454 data, using both for contig and scaffolding): | ||
+ | * k31: | ||
+ | * 1,298,372 scaffolds from 4,814,226 contigs sum up 632,702,276bp, with average length 487, 0 gaps filled | ||
+ | * 3,611,844 scaffolds&singleton sum up 1,133,413,022bp, with average length 313 | ||
+ | * the longest is 10,340bp,scaffold N50 is 442 bp, scaffold N90 is 148 bp | ||
+ | * k47: | ||
+ | * 871,819 scaffolds from 5,306,463 contigs sum up 530,762,874bp, with average length 608, 0 gaps filled | ||
+ | * 4,203,195 scaffolds&singleton sum up 1,296,678,043bp, with average length 308 | ||
+ | * the longest is 14,750bp,scaffold N50 is 458 bp, scaffold N90 is 140 bp | ||
+ | * k63: | ||
+ | * 270,887 scaffolds from 4,022,505 contigs sum up 139,720,415bp, with average length 515, 0 gaps filled | ||
+ | * 3,710,532 scaffolds&singleton sum up 690,332,560bp, with average length 186 | ||
+ | * the longest is 14,897bp,scaffold N50 is 232 bp, scaffold N90 is 112 bp | ||