Banana Slug Genomics

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[[feed.php|{{ :feed-icon-28x28.png}}]] ====== Banana slug genomics ====== ===== 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. * [[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. ===== 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 | Un | DiscovarDeNovo/firstFullRun/discovarDeNovoAssembly.fasta | ---- {{http://users.soe.ucsc.edu/~karplus/cyberslugs/slug-dreaming-300x400.jpg }}((The Cyberslug is **not** licensed under Creative Commons. It is licensed exclusively to the Jack Baskin School of Engineering at the University of California, Santa Cruz, and may not be used by others. Furthermore, the slug-dreaming icon here is only for use by the Banana Slug Genomics project—contact Kevin Karplus for permission to use it.)) This is the home page for the Banana Slug Genomics wiki. Material on these pages will mainly be created by students of the [[http://users.soe.ucsc.edu/~karplus/bme235|BME235 course]]. We hope to be able to assemble and annotate the genome of the UCSC mascot //Ariolimax dolichophallus//, the slender banana slug, as well as collecting all the information we can find about the biology of the banana slug. This wiki should be publicly readable, but editable only by people with UCSC School of Engineering computer accounts. Contact Kevin Karplus (karplus@soe.ucsc.edu) if you need to edit these pages and do not have such an account. In addition to page-specific discussions on each page, there is a separate [[http://forums.soe.ucsc.edu/viewforum.php?f=102|forum]] for discussions about the class. The discussion forum is intended for more transient discussions than this wiki---such as where new material should go into the wiki, discussions of re-organizing the wiki or alerts about time-sensitive material. ===== Old pages of this wiki ===== These links are several years old. Due to the speed in which bioinformatics moves, most if not all of this information will be outdated. * [[RNA]] * [[computer_resources:data|Data available]] lists the datasets that we have to assemble and annotate the genome. The data will not appear on the wiki itself (due to the size of the files), but descriptions of it and pointers to the files will. * [[computer_resources:assemblies|Assemblies]] lists the attempted assemblies (separated into subdirectories by organism). * [[Lab protocols]] will describe how the slugs were collected, the DNA extracted, and all the wet-lab work was done to produce the data files. * [[Sequencing technologies]] lists the platforms used for getting data on the banana slug. From there, we'll have pages on each technology explaining how it works, what sort of data it produces, what its common errors modes are, and other information needed to work with the data. * [[Bioinformatic tools]] lists the available tools for assembly and annotation. Each tool will have its own web page describing its strengths and weaknesses, and what we managed to do using that tool. * [[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. * [[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.