Banana Slug Genomics

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======Summer 2015======

====Volunteers====
Students continuing to Work in the summer.
please include a note that briefly describes something you are currently studying or doing for the project

| Name | E-mail | Team | Lab | note |
| Jared C | jcopher@ucsc.edu | ABySS | Pourmand | Banana Slug Biology and Mollusk genomics |
| Siddra H | sihussai@ucsc.edu | ABySS | Green | |
| Emilio F | efeal@ucsc.edu | ABySS | | |
| Charles M | cmarkell@ucsc.edu | SOAP | Haussler | |
| Natasha | ndudek@ucsc.edu | Discovar | Shapiro | I want to work on finishing the mitochondrion assembly |
| Chris Eisenhart | ceisenha@ucsc.edu | Discovar | Browser Group | Get it on the browser, finish the assembly with Sspace. I wont be at the meetings as I have to work, I will correspond over email. |
|Christopher Kan|chkan@ucsc.edu|SGA|Pogson|Will finish SGA Assembly|
| Nedda | nsaremi@ucsc.edu | SOAP | Green |
| Josh | jolespin@ucsc.edu | SGA | Bernick |Once a good assembly is generated and we get a transcriptome, I can try and extract the exons, introns, and genes (5'UTR, CDS, 3'UTR).  I wrote some scripts that can do this and confirms with exon-junction motifs.  Can't meet weekly since I'll be in SD. |
|Robert|calef@soe.ucsc.edu|Discovar|Green|Will start looking into running SOAP gap closer on the Kolossus Discovar assembly, as well as tools for scaffolding with RNA-seq data|
|Charles| chkcole@ucsc.edu| Meraculous| Vollmers| I'm currently working on getting the RNA-Seq data. We have some preliminary stuff I just need to process it and confirm the quality of the libraries. Also, repetitive elements.|


====Schedule of meetings====

Suggestions for weekly meetings:

  * Meet in PSB 305 (same classroom)
  * once a week
  * Weds at 1:30pm



====Agenda Items====

A list of unresolved tasks

  * distribute T-shirts (These should be available in the afternoon of 9 June 2015.)
  * Apply SOAPdenovo scaffolding and gap filling to Discovar scaffolds
  * Merge assemblies
  * Decide on a final assembly from working assemblers: that's going to be a moving target as we add more data and analyses. We may have to freeze one for annotation work, but there's not much point to doing this before we've finished all the scaffolding we can do, as our scaffolds are still quite small (about 12k for the scaffold N50 as of 2015 June 8).
  * RNAseq:
    * Using RNAseq data to test existing scaffolding
    * Transcriptome assembly
    * Using RNASeq data for scaffolding
  * Annotations
  * Heterozygosity: assuming that Ed's initial result (which is not yet on the wiki) holds up, that the collected slug was almost purely homozygous, then we have the interesting question whether the UCSC slug population is so inbred that it is nearly clonal.
  * Phylogeny: not clear what we can add here—there aren't enough mollusk genomes around for phylogenetic analysis to say much.  What meaningful questions might we answer?
  * Non-slug DNA in reads: part of annotation is going to be identifying and removing contaminants.
  * Repeats
    * Using RepARC (or building new tools) to construct highly repetitive contigs
    * Scaffolding and gap filling on highly repetitive contigs to build full repeat consensus (and variants)
    * Annotating repeats (viral and bacterial contaminants, mitochondrion, transposons, … )
  * Mitochondrion assembly
    * PCR to close gaps
    * studying graph of contig neighbors to try to determine order without PCR
  * Use of old data (2010 and 2011 classes:  There is not really much data there, and the quality is not very high, so there may not be much point in trying to use it.  Perhaps mapping it could find some variation—we might like to know whether the UCSC slug population is nearly clonal.


Longer term: we'll need to decide whether we need more data, particularly for scaffolding.  Will Ed's lab be continuing to develop a new mate-pair library procedure, which could give us new libraries to work with?  Will the MinION deliver higher-throughput long reads this year, and can we get a run of long DNA through the MinION?

====Finished Work====

A list of work completed since BME235 ended:

  * Disovar assembly with all shotgun data, accomplished on Kolussus
  * SOAPdenovo assembly with all shotgun data and gap closed, accomplished on edser2
Banana Slug Genomics

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