Banana Slug Genomics

====== Banana slug genomics ====== {{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 [[https://www.soe.ucsc.edu/people/karplus | Kevin Karplus]] for permission to use it.)) **This is the home page for the Banana Slug Genomics wiki. ** **We are working to assemble and annotate the genome of the UCSC mascot //Ariolimax dolichophallus//, the slender banana slug. Additionally we are collecting and hosting as much information as we can about the biology of the banana slug.** Researchers and staff at UCSC created this [[https://www.youtube.com/watch?t=11&v=hF8IkJpq6OI | video ]] for the 2014 crowdfunding campaign. See how the project started and follow along at a high level, a great place to start for those uninitiated in genomics! This project is hosted at UCSC as a graduate class BME235. All information is publicly accessible and free to use, please cite the authors when possible and the wiki as a whole. Please contact [[https://www.soe.ucsc.edu/people/karplus | Kevin Karplus]] with general questions. For questions on specific assemblies please identify the team that created the assembly and email them directly. ===== About the slug ===== //Ariolimax dolichophallus// is a relatively unstudied species. Here we aim to provide concise and accurate biological information about //Ariolimax dolichophallus//. [[about_the_slug:about_the_slug| About the slug ]] [[Banana_Slug_Dissection | Banana Slug Dissection]] ===== Data ===== Links to the raw [[data_overview:data_overview| data]], as well as processed data are provided [[data_overview:data_overview| here]]. The data includes mate-pair data, raw Illumina reads, and RNA-seq. [[data_overview:data_overview| Data]] ===== Assemblies ===== The [[assemblies:assemblies| assemblies ]] are available for annotation, merging and other bioinformatics uses. The assemblies include full nuclear assemblies as well as mitochondrion assemblies. [[assemblies:assemblies| Assemblies ]] ===== Post-assembly analysis ===== Our [[post-assembly_analysis:post-assembly_analysis|analysis]] of the completed assemblies. Includes the [[post-assembly_analysis:banana_slug_genome_browser|UCSC assembly hub for the banana slug]], analysis of heterozygosity, the [[post-assembly_analysis:2015:rna_scaffolding | RNA scaffolding efforts]] and any progress made on gene finding/annotation. [[post-assembly_analysis:post-assembly_analysis| Post-assembly analysis ]] ===== About the class ===== The project is supported at UCSC as the BME235 Banana Slug Genomics class. More information about the class can be found in the [[about_the_class:about_the_class| general information]] link. To see which students have worked on the project view the [[contributors:contributors| contributors ]] link. The budget for the project is publicly viewable using the [[about_the_class:budget| budget]] link. Old pages, pages that do not follow the style guide, and pages that cannot be assimilated into the main wiki are archived [[archive:archive| here]]. [[about_the_class:about_the_class| About the class ]] [[contributors:contributors| Contributors]] [[about_the_class:budget| Budget]] [[archive:archive| Archive]] Currently we **are not** accepting donations. Thanks to all our past donors! ---- This wiki is publicly readable, but editable only by people with UCSC School of Engineering computer accounts. Contact [[https://www.soe.ucsc.edu/people/karplus | Kevin Karplus]] 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.