assemblies:assemblies
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assemblies:assemblies [2015/07/16 18:56] ceisenhart Major changes under way, please let me finish before doing more |
assemblies:assemblies [2015/08/19 20:14] (current) chkcole |
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| =====2015===== | =====2015===== | ||
| + | ====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==== | ||
| + | [[natasha@dudek.org |Natasha Dudek]] (Discovar //de novo//) re-assembled the [[assemblies::2015::mitochondrion_assembly | mitochondrion]] in 2015. | ||
| - | [[natasha@dudek.org |Natasha Dudek]] re-assembled the mitochondrion in 2015 using data from the 2011 and 2010 class as well as new data. | + | | 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===== | ||
| - | [[https://users.soe.ucsc.edu/~karplus/| Kevin Karplus]] attempted a [[2011::mitochondrion_assembly]] in 2012 using the data he had previously gathered. | + | ====Mitochondrion==== |
| + | [[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.1437072986.txt.gz · Last modified: 2015/07/16 18:56 by ceisenhart
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