archive:computer_resources:assemblies
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archive:computer_resources:assemblies [2010/05/19 20:45] galt Assembled Slug Genome from Illumina Paired with SOAPdenovo |
archive:computer_resources:assemblies [2010/05/19 20:49] galt |
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| * Final graph has 3602 nodes and n50 of 4851, max 94854, total 1767903, using 28785664/61262410 reads | * Final graph has 3602 nodes and n50 of 4851, max 94854, total 1767903, using 28785664/61262410 reads | ||
| * SOAPdenovo | * SOAPdenovo | ||
| - | * SOAPdenovo-assembly1/ Assembling Pog 454 long reads with SOAPdenovo. After being simply unable to get any version of the program to read a FASTA file despite documentation examples, I finally found a utility sff2fastq that made it possible to run SOAPdenovo on Pog 454 fastq. I have not had time to optimize parameters yet. The largest contig made with default params was just 4k. | + | * SOAPdenovo-assembly1/ Assembling Pog 454 long reads with SOAPdenovo. After being simply unable to get any version of the program to read a FASTA file despite documentation examples, I finally found a utility sff2fastq that made it possible to run SOAPdenovo on Pog 454 fastq. I have not had time to optimize parameters yet. The largest contig made with default params was just 4k. Later raised cutoff to 12 and got maxcontig of 70k. Could not run the scaffold step because it crashed, probably because it was written for short 52bp solexa reads and the long 454 reads are messing it up. |
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| * It was used to assemble the Panda genome by BGI. | * It was used to assemble the Panda genome by BGI. | ||
| * Used kolossus which has 1TB and 64cpus. | * Used kolossus which has 1TB and 64cpus. | ||
| - | * Ran with k=31 an k=23. k=31 was better (9k maxcontig) | + | * Ran with k=31 and k=23. k=31 was better (9k maxcontig) |
| * 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. | ||
archive/computer_resources/assemblies.txt · Last modified: 2015/09/02 16:53 by 92.247.181.31
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