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start [2015/07/15 18:50] ceisenhart Major changes under way, please let me finish before doing more |
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**This is the home page for the Banana Slug Genomics wiki. ** | **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 find about the biology of the banana slug.** | + | **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! | 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. | 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 Dolicophallus// is a relatively unstudied species. Here we aim to provide concise and accurate biological information about //Ariolimax Dolicophallus//. | ||
+ | |||
+ | [[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 ===== | ===== 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 ]] | ||
- | [[Full_genome_assemblies | Full genome assemblies ]] | ||
- | [[Mitochondrion_assemblies | Mitochondrion assemblies ]] | ||
- | ===== Data ===== | ||
- | [[Data overview | Access to the raw and processed data]] | ||
===== About the class ===== | ===== 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 ]] | ||
- | [[About the class | General information about the class and wiki ]] | + | [[contributors:contributors| Contributors]] |
- | [[Teams | Pages for each assembly team ]] | + | [[about_the_class:budget| Budget]] |
- | [[Budget | The budget for our project]] | + | [[archive:archive| Archive]] |
- | Currently we **are not** accepting donations. Thanks to all our current and previous donors! | + | Currently we **are not** accepting donations. Thanks to all our past donors! |
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