archive:computer_resources:assemblies
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archive:computer_resources:assemblies [2010/04/30 23:01] karplus added mention of trim9.joins for the homework. |
archive:computer_resources:assemblies [2010/05/19 20:45] galt Assembled Slug Genome from Illumina Paired with SOAPdenovo |
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| * The output has 2664 contigs, comprising 443,648 bases (still less than the de novo assembly). | * The output has 2664 contigs, comprising 443,648 bases (still less than the de novo assembly). | ||
| * The longest contig is only 1876 bases. | * The longest contig is only 1876 bases. | ||
| + | * SOAPdenovo-assembly1/ First run of SOAPdenovo on illumina paired ends. | ||
| + | * SOAPdenovo requires fastq input files. | ||
| + | * It was used to assemble the Panda genome by BGI. | ||
| + | * Used kolossus which has 1TB and 64cpus. | ||
| + | * Ran with k=31 an k=23. k=31 was better (9k maxcontig) | ||
| + | * so ran with filling -R to get 12k maxcontig. | ||
| + | * Then ran the scaffolding steps with 200bp insert size. | ||
| + | * For all steps, used low default cutoffs since our 10x coverage | ||
| + | * is not high. 21k max scaffold size. Estimated | ||
| + | * genome size is around 3G. The 4 steps are | ||
| + | * 1. pregraph (3.5 to 4.5 hours for 30 to 60 cpus) | ||
| + | * 2. contig (1.3 hours) | ||
| + | * 3. map (0.6 hours with 60cpus) - paired ends | ||
| + | * 4. scaff (1 hour with 60cpus) | ||
archive/computer_resources/assemblies.txt · Last modified: 2015/09/02 16:53 by 92.247.181.31
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