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assemblies:assemblies [2015/07/16 18:57]
ceisenhart [Mitochondrion]
assemblies:assemblies [2015/08/19 20:14] (current)
chkcole
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 ====Nuclear==== ====Nuclear====
 | Contributing team | Contig N50 | Scaffold N50 | Total bases | Location |  | Contributing team | Contig N50 | Scaffold N50 | Total bases | Location | 
-|[[::​team_2_page|SOAP:​ Team 2 page]]| 8,033 | 11,000 | 2,​293,​889,​058 | | +|[[contributors:​team_2_page|SOAP:​ Team 2 page]]| 8,033 | 11,000 | 2,​293,​889,​058 |  ​http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Assemblies/​2015/​SOAPdenovo2/​SOAPdenovo2_run3_all/​soapdenovo2_allAssembly_1.scafSeq.gapclosed ​
-|[[::​team_4_page| ABySS: Team 4 page]]| 2,669 | 3,063 | 2,​446,​362,​204| +|[[contributors:​team_4_page| ABySS: Team 4 page]]| 2,669 | 3,063 | 2,​446,​362,​204| http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Assemblies/​2015/​abyss/​slug-scaffolds.fa ​
-|[[::​team_5_page| Discovar de novo: Team 5 page]]| 10,427 | 12,549 | 2,​395,​797,​282 |  |+|[[contributors:​team_5_page| Discovar de novo: Team 5 page]]| 10,427 | 12,549 | 2,​395,​797,​282 | http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Assemblies/​2015/​DiscovarDeNovo/​KolossusAssembly/​discovarDeNovoKolossusAssembly.fasta ​|
 ====Mitochondrion==== ====Mitochondrion====
-[[natasha@dudek.org |Natasha Dudek]] re-assembled the [[2015::​mitochondrion_assembly | mitochondrion]] in 2015 using data from the 2011 and 2010 class as well as new data+[[natasha@dudek.org |Natasha Dudek]] ​(Discovar //de novo//​) ​re-assembled the [[assemblies::​2015::​mitochondrion_assembly | mitochondrion]] in 2015.
  
 +| Contributing team | Contig N50 | Scaffold N50 | Total bases | Location |
 +| [[contributors:​team_5_page| Discovar de novo: Team 5 page]] | 9,030 | 9,030 | 15,548 | http://​genome-test.cse.ucsc.edu/​~charles/​BME235_backup/​Data/​2015/​mitochondrion/​mitochondrion_SW018-9_discovar.fasta | 
  
 +
 +[[assemblies::​2015::​mitochondrion_assembly | The 2015 mitochondrion assembly page]]
 +
 +====Repetitive Elements====
 +| Contributing team | Contig N50 | Scaffold N50 | Total bases | Location |
 +|Charles Cole|29|29|19,​510,​691|campusrocks.ucsc.edu:/​campusdata/​BME235/​S15_assemblies/​RepArk/​Banana_Slug_Repetitive_elements_without_UCSF/​velvet_repeat_lib/​contigs.fa|
 +[[assemblies::​2015::​repetitive_elements|2015 repetitive Elements page]]
 =====2011===== =====2011=====
 ====Mitochondrion==== ====Mitochondrion====
-[[https://​users.soe.ucsc.edu/​~karplus/​| Kevin Karplus]] attempted a [[2011::​mitochondrion_assembly |mitochondrion assembly]] in 2012 using the data he had previously gathered. ​+[[https://​users.soe.ucsc.edu/​~karplus/​| Kevin Karplus]] attempted a [[assemblies::​2011::​mitochondrion_assembly |mitochondrion assembly]] in 2012 using the data he had previously gathered. ​ 
 + 
 +| Contributing team | Contig N50 | Scaffold N50 | Total bases | Location | 
 +| [[https://​users.soe.ucsc.edu/​~karplus/​| Kevin Karplus]] |  |  |  | {{:​computer_resources:​assemblies:​mitochondrion-draft2.fasta.gz|}} |  
 + 
 +[[assemblies::​2011::​mitochondrion_assembly | The 2012 mitochondrion assembly page ]] 
  
-[[2011::​mitochondrion_assembly | The 2012 mitochondrion assembly ]]  
 =====2010===== =====2010=====
  
  
  
assemblies/assemblies.1437073066.txt.gz · Last modified: 2015/07/16 18:57 by ceisenhart