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| [[Mitochondrion_assemblies | Mitochondrion assemblies ]] | [[Mitochondrion_assemblies | Mitochondrion assemblies ]] | ||
| - | [[mitochondrion_2015 | 2015 Mitochondrion assembly ]] | ||
| - | ===== Raw data ===== | + | ===== Data ===== |
| - | Data overview page | + | [[Data overview | Access to the raw and processed data]] |
| ===== About the class ===== | ===== About the class ===== | ||
| - | About the class | + | [[About the class | General information about the class and wiki ]] |
| - | Team pages | + | [[Teams | Pages for each assembly team ]] |
| - | Budget | + | [[Budget | The budget for our project]] |
| - | + | Currently we **are not** accepting donations. Thanks to all our current and previous donors! | |
| - | [[feed.php|{{ :feed-icon-28x28.png}}]] | + | |
| - | + | ||
| - | ===== 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. | + | |
| - | + | ||
| - | * [[Spring 2015 syllabus]] The lecture schedule and registered note takers. | + | |
| - | * [[Data overview]] Raw data and associated analysis. | + | |
| - | * [[Teams]] Each team is attempting an assembly with a different program. | + | |
| - | * [[Summer 2015]] A page to organize summer work. | + | |
| - | * [[Style Guide|Complete guide for modifying the wiki]] | + | |
| - | * [[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. | + | |
| - | * [[Backup directory]] Paths on Charles' hive account where assembly and raw data files are backed-up. | + | |
| - | + | ||
| - | ===== 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. | + | |
| - | * [[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. | + | |
| - | * [[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. | + | |
| - | * [[Euchromatin and Heterochromatin]] | + | |
| - | + | ||
| - | ====Team pages and results ==== | + | |
| - | The mitochondrion for the banana slug was assembled! | + | |
| - | + | ||
| - | [[mitochondrion_2015 | 2015 Mitochondrion assembly ]] | + | |
| - | + | ||
| - | 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]]| 8,033 | 11,000 | 2,293,889,058 (non gap approx) | SOAPdenovo2/assemblyTask/SOAPdenovo2_run3_all/soapdenovo2_allAssembly_1.scafSeq.gapclosed| | + | |
| - | |[[0.10.13|SGA: Team 3 page]]| N/A | N/A | N/A | N/A | | + | |
| - | |[[team_4_page| ABySS: Team 4 page]]| 2,669 | 3,063 | 2,446,362,204| | + | |
| - | |[[team_5_page| Discovar de novo: Team 5 page]]| 10,427 | 12,549 | 2,395,797,282 | DiscovarDeNovo/KolossusAssembly/discovarDeNovoKolossusAssembly.fasta | | + | |
start.txt · Last modified: 2015/10/07 03:14 by karplus
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