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contributors:team_5_page [2015/05/21 19:35]
ceisenhart
contributors:team_5_page [2015/08/04 01:33]
66.249.79.241 ↷ Links adapted because of a move operation
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 Discovar //de novo// is a next generation sequence assembly program. The program was developed by the Broad Institute and was released late in 2014. Discovar //de novo// is designed for 250 bp long illumina reads with the PCR duplicates and adaptor sequences removed. The following webpage contains the manual as provided by the Broad Institute (http://​www.broadinstitute.org/​software/​discovar/​blog/​):​ Discovar //de novo// is a next generation sequence assembly program. The program was developed by the Broad Institute and was released late in 2014. Discovar //de novo// is designed for 250 bp long illumina reads with the PCR duplicates and adaptor sequences removed. The following webpage contains the manual as provided by the Broad Institute (http://​www.broadinstitute.org/​software/​discovar/​blog/​):​
  
-[[Discovar //de novo// manual:Discovar de novo manual]].+[[team_5_page:discovar_de_novo_manual]].
  
  
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 |[[team_5_page:​50PerRun | 50% data]]| (Post Skewer and FastUniq) MiSeq data SW019_S1_L001,​ HiSeq data SW018_S1_L007,​ HiSeq data SW019_S2_L008 | |[[team_5_page:​50PerRun | 50% data]]| (Post Skewer and FastUniq) MiSeq data SW019_S1_L001,​ HiSeq data SW018_S1_L007,​ HiSeq data SW019_S2_L008 |
 |[[team_5_page:​50PerRunUCSF | 50% data UCSF]]| (Post Skewer and FastUniq) UCSF SW018 and SW019 data | |[[team_5_page:​50PerRunUCSF | 50% data UCSF]]| (Post Skewer and FastUniq) UCSF SW018 and SW019 data |
 +|[[team_5_page:​FullRun1 | Full data run 1]] | (Post Skewer and FastUniq) 100% of the MiSeq SW019, UCSF SW019, and 50 % BS-tag datasets |
 +|[[team_5_page:​KollosusFullRun | Kolossus full run]] | (Post Skewer and FastUniq) 100% of the MiSeq SW019, UCSF SW019, UCSF SW018, BS-tag, BS-MK datasets |
  
 The logs are very large, important statistics have been gathered and are compared below. ​ The logs are very large, important statistics have been gathered and are compared below. ​
 Note that MPL1 is an acronym for mean length of first read in pair up to first error.  ​ Note that MPL1 is an acronym for mean length of first read in pair up to first error.  ​
-| | 1% run | 5% run | 10 % run| 50 % run | 50% UCSF run |  +| | 1% run | 5% run | 10 % run| 50 % run | 50% UCSF run | FullRun1 | Kollosus full run |  
-| Total runtime | 1.75 hours| 1.53 hours| 2.4 hours| 8.53 hours| 14.9 hours |  +| Total runtime | 1.75 hours| 1.53 hours| 2.4 hours| 8.53 hours| 14.9 hours | 24.2 hours| 103 hours |    
-| Peak memory use | 43.92 GB | 78.10 GB| 151.05 GB| 220.11 GB | 184.09 GB|  +| Peak memory use | 43.92 GB | 78.10 GB| 151.05 GB| 220.11 GB | 184.09 ​GB| 246.03 GB| 583.25 ​GB | 
-| Bases in 1kb+ scaffolds| 75,233 | 592,685 | 1,476,875 |  101,397,871 | 1,​528,​625,​509 | +| Bases in 1kb+ scaffolds| 75,233 | 592,685 | 1,476,875 |  101,397,871 | 1,​528,​625,​509 ​| 1,​849,​167,​875 | 1,​885,​373,​341
-| Bases in 10kb+ scaffolds| 10,572 | 11,088 | 168,543 | 151,417 | 137,959,107 | +| Bases in 10kb+ scaffolds| 10,572 | 11,088 | 168,543 | 151,417 | 137,​959,​107 ​| 972,798,485 | 1,​106,​140,​476 ​
-| MPL1 | 2 | 2 | 3 | 7 | 156 | +| MPL1 | 2 | 2 | 3 | 7 | 156 | 169 | 169 |  
-| Contig N50 | 2,622 | 2,067 | 2,563 | 1,489  | 3,979 |  +| Contig N50 | 2,622 | 2,067 | 2,563 | 1,489  | 3,979 | 9,513 | 10,​427 ​|  
-| Scaffold N50 | 2,622 | 2,067 | 2,563 | 1,489  | 3,979 | +| Scaffold N50 | 2,622 | 2,067 | 2,563 | 1,489  | 3,979 | 10,634 | 12,549 |  
 +| Coverage | | | | | 16x | 47x | 80X 
  
 ====Fasta assemblies==== ====Fasta assemblies====
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 |50%run| 137 M | 137,695,736 | 273,653 | 1,006 | 19,658 | 1,489 | | 151,417 |  |50%run| 137 M | 137,695,736 | 273,653 | 1,006 | 19,658 | 1,489 | | 151,417 | 
 |UCSF50%run | 1.9 G | 1,​839,​371,​352 | 1,126,557 | 1,632| 55,757 | 3,979 | 80,721 | 137,959,107 | |UCSF50%run | 1.9 G | 1,​839,​371,​352 | 1,126,557 | 1,632| 55,757 | 3,979 | 80,721 | 137,959,107 |
-|FullRun1 ​| 2.2G | | 10,634 | | 972,798,485 | +|firstFullRun ​| 2.2G | 2,​245,​788,​654 ​1,​450,​447 ​1,548 153,​999 ​| 10,634 | 118,​545 ​| 972,798,485 | 
 +|Kolossus full run | 2.4G | 2,​395,​797,​282 | 1,843,153 | 1299 | 129,831 | 12,549 | 113,978 | 1,​106,​140,​476 | 
 + 
 +The absolute path to our latest assembly in .fasta format is; 
 + 
 +/​campusdata/​BME235/​S15_assemblies/​DiscovarDeNovo/​KolossusAssembly/​discovarDeNovoKolossusAssembly.fasta
  
 Looking at the 10% run, the majority of scaffolds generated are quite short (<​1kb).  ​ Looking at the 10% run, the majority of scaffolds generated are quite short (<​1kb).  ​
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 {{:​histogram_for_ucsf_50_run.png?​200|}} {{:​histogram_for_ucsf_50_run.png?​200|}}
- + 
-The banana slug genome is estimated to be 2.1 billion bases (2,800 million), our latest run has assembled just under 2 billion bases! ​+
  
 ====Post assembly scaffolding==== ====Post assembly scaffolding====
 The program SSPace (documentation below) was used to scaffold the the assembly with mate pair data. The UCSF SW041 and SW042 mate pair libraries were used to generate the library.txt file.  The program SSPace (documentation below) was used to scaffold the the assembly with mate pair data. The UCSF SW041 and SW042 mate pair libraries were used to generate the library.txt file. 
  
-[[team_5_page:​SSPaceSummaryFile | SSpace summary file ]] +[[team_5_page:​SSPaceSummaryFile | SSpace summary file UCSF 50% ]]  
 + 
 +[[team_5_page:​SSPaceSummaryFile2 | SSpace summary file firstFullRun ​]] 
  
  
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 See instructions for setting up the hub here,  See instructions for setting up the hub here, 
-[[banana_slug_genome_browser |Banana slug browser ]]+[[post-assembly_analysis:​banana_slug_genome_browser|Banana slug browser ]]
  
  
contributors/team_5_page.txt · Last modified: 2015/09/04 07:56 by 157.55.39.159