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contributors:team_5_page [2015/05/27 16:38]
ceisenhart [Post assembly scaffolding]
contributors:team_5_page [2015/08/04 08:33]
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 BS-tag datasets |+|[[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 | FullRun1 |  +| | 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 | 24.2 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| 246.03 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 | 1,​849,​167,​875 | +| 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 | 972,798,485 | +| 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 | 169 |  +| MPL1 | 2 | 2 | 3 | 7 | 156 | 169 | 169 |  
-| Contig N50 | 2,622 | 2,067 | 2,563 | 1,489  | 3,979 | 9,513 | +| 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 | 10,634 | +| Scaffold N50 | 2,622 | 2,067 | 2,563 | 1,489  | 3,979 | 10,​634 ​| 12,​549 ​|  
-| Coverage | | | | | 16x | 47x | +| 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 |
-|firstFullRun | 2.2G | 2,​245,​788,​654 | 1,450,447 | 1,548 | 153,999 | 10,634 | 118,545 | 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; The absolute path to our latest assembly in .fasta format is;
  
-/​campusdata/​BME235/​S15_assemblies/​DiscovarDeNovo/​firstFullRun/discovarDeNovoAssembly.fasta+/​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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 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 14:56 by 157.55.39.159