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| - | ====== Banana Slug Genomics ====== | + | ====== Banana slug genomics ====== |
| ===== Reborn - Spring 2015 ===== | ===== Reborn - Spring 2015 ===== | ||
| Welcome back, Banana Slug Genomics! Following the successful [[https://crowdfund.ucsc.edu/project/5424db950920652635292bae|crowdfunding campaign]], this class and effort will be rebooted. | Welcome back, Banana Slug Genomics! Following the successful [[https://crowdfund.ucsc.edu/project/5424db950920652635292bae|crowdfunding campaign]], this class and effort will be rebooted. | ||
| - | * [[Spring 2015 Syllabus]] The lecture schedule and registered note takers. | + | * [[Spring 2015 syllabus]] The lecture schedule and registered note takers. |
| * [[Data overview]] Raw data and associated analysis. | * [[Data overview]] Raw data and associated analysis. | ||
| * [[Teams]] Each team is attempting an assembly with a different program. | * [[Teams]] Each team is attempting an assembly with a different program. | ||
| * [[Style Guide|Complete guide for modifying the wiki]] | * [[Style Guide|Complete guide for modifying the wiki]] | ||
| * [[computer_resources:campusrocks|Complete guide to campusRocks and SGE]] | * [[computer_resources:campusrocks|Complete guide to campusRocks and SGE]] | ||
| + | * [[Budget]] | ||
| + | * [[Specific task]] | ||
| + | * [[Banana slug genome browser]] A guide for accessing and setting up the banana slug hub. | ||
| ===== Important pages of this wiki ===== | ===== Important pages of this wiki ===== | ||
| * [[Computer resources]] describes the computers and file systems available for this class, how to get an account, how the directories are organized, how to get file permissions set correctly, and so forth. | * [[Computer resources]] describes the computers and file systems available for this class, how to get an account, how the directories are organized, how to get file permissions set correctly, and so forth. | ||
| - | * [[Banana Slug Genome Browser]] will have a UCSC genome browser, once we get to the point of having few enough contigs that building a browser makes sense. | ||
| * [[Style guide]] will have suggestions for organizing content on the wiki. | * [[Style guide]] will have suggestions for organizing content on the wiki. | ||
| * [[Lecture notes]] will have pointers to notes taken by the students for each lecture. Two students will be designated each lecture to take notes, but others are encouraged to add their own notes to the wiki pages. | * [[Lecture notes]] will have pointers to notes taken by the students for each lecture. Two students will be designated each lecture to take notes, but others are encouraged to add their own notes to the wiki pages. | ||
| + | * [[Other mollusk genomes]] has a list of other mollusks that have been sequenced, and where the data for them is. Prior mollusk genomes may be very useful in annotating the banana slug. | ||
| + | * [[RNA]] | ||
| + | * [[Euchromatin and Heterochromatin]] | ||
| + | |||
| + | ====Team pages and results ==== | ||
| + | The mitochondrion for the banana slug was assembled! | ||
| + | |||
| + | [[mitochondrion_2015 | 2015 Mitochondrion assembly ]] | ||
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| + | Each team is attempting to assemble the banana slug genome with a different assembly program. The results are posted in the team pages below. The assemblies are in the /campusdata/BME235/S15_assemblies/ folder on the campusrocks server. | ||
| + | | Team page | Contig N50 | Scaffold N50 | Total bases | Path | | ||
| + | |[[team_1_page| Meraculous: Team 1 page]]| N/A | N/A | N/A | N/A | | ||
| + | |[[soapdenovo2|SOAP: Team 2 page]]| 1,425 | 9,501 | 2,385,757,551 | SOAPdenovo2/assemblyTask/SOAPdenovo2_run2/soapdenovo2_sparseGraph_2.scafSeq| | ||
| + | |[[0.10.13|SGA: Team 3 page]]| | | ||
| + | |[[team_4_page| ABySS: Team 4 page]]| 2,669 | 3,063 | 2,446,362,204| | ||
| + | |[[team_5_page| Discovar de novo: Team 5 page]]| **9,513** | **10,634** | 2,245,788,654 | DiscovarDeNovo/firstFullRun/discovarDeNovoAssembly.fasta | | ||
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| * [[Banana slug biology]] collects the information we can find about the biology of //Ariolimax dolichophallus// (and other //Ariolimax// species). | * [[Banana slug biology]] collects the information we can find about the biology of //Ariolimax dolichophallus// (and other //Ariolimax// species). | ||
| * [[Banana slugs in popular culture]] collects random information about banana slugs that can't really be classified as "biology". This will probably contain mainly information about the slug as the UCSC mascot. | * [[Banana slugs in popular culture]] collects random information about banana slugs that can't really be classified as "biology". This will probably contain mainly information about the slug as the UCSC mascot. | ||
| - | * [[Other mollusk genomes]] has a list of other mollusks that have been sequenced, and where the data for them is. Prior mollusk genomes may be very useful in annotating the banana slug. | ||
| * [[Contributors]] will list the main contributors to this project (providing pictures and links to their own pages as appropriate). | * [[Contributors]] will list the main contributors to this project (providing pictures and links to their own pages as appropriate). | ||
| * [[Review Articles]] will list helpful review articles discovered. | * [[Review Articles]] will list helpful review articles discovered. | ||
start.txt ยท Last modified: 2015/10/07 03:14 by karplus
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