Dec09 KembelNotes Kembel Notes

Aaron Darling

Phylogenetic cobinning

• Illumina GAII can generate huge quantities of data for cheap - but they are short 80bp reads
• We want to place these reads on a reference phylogeny i.e. with pplacer
• Deep sequencing means multiple reads can come from the same organisms
• We may want to group together these similar sequences from the same/similar organisms and place them as a group onto the reference phylogeny
• Model linkage - a model of of partitioning all reads into sets that are linked (can be thought of as coming from same organism). Place these linked reads onto the reference phylogeny as a single leaf.
• Evaluate likelihood of different ways of partitioning set of all reads into linkage groups. Model linkage group size as coming from a gamma distribution, estimate parameters of the distribution with likelihood, figure out most likely way to cobin reads into linkage groups.
• Overall this approach allows the reads to share phylogenetic information among one another which can improve overall phylogenetic signal and improve placement of reads in a phylogenetic context
• Discussion points
  • Not yet implemented
  • Will require massive compute power - GSoC project using graphics card parallel computing may help
  • What about reads with no similarity to known genomes? Can we use paired ends?
  • Difference in rates of evolution
  • Lateral gene transfer
  • What does a linkage group mean - is it a 'species' or 'OTU'?
  • Other sources of linkage information available?
  • Will any of this matter with PacBio sequencing technology?

Data sets and metadata

• Should we set up a MySQL database that everyone can use to store, share and subset data?
• This will make it easier to make sure that people are working from the same version of data
• We will encourage people to provide metadata for all the data in the database
  • Look into EML and metadata standards from NCEAS (ecoinformatics.org)
• Especially important for sharing code - we are probably reinventing the wheel
  • Let's share scripts on iSEEM SVN - currently they mostly live on genbeo.
  • Document script names and descriptions on the wiki here.

Informatics issues / jobs

1. IT issues
   • Guillaume will be point man for issues related to genbeo/cluster use
2. Data / databases
3. Scripts / tools / software
4. Task tracking / management / jobs / working
   • Ask slashdot what to use?
5. CAMERA
   • Guillaume will be point man for CAMERA interactions
6. Developing
7. Wiki
   • We need to update the public wiki page on OpenWetWare - someone (Guillaume?) fix this, contact OWW
   • Fine to start migrating content from private -> public
   • We all need to be updating the wiki on a regular basis with a summary of what we've been doing, with enough detail that someone can figure out what you've been doing and eliminate duplication of effort
8. Citeulike
   • Please share papers you're reading on citeulike - either in your own library or in the iseem group
     • There's a bookmarklet and a way to post stuff from google reader to citeulike
9. Communication system
   • Email list? Online forum? Gmail group?
10. Software packages and locales
    • Let's set up a shared /bin directory on genbeo

Specific data requests

• Josh
  • OTUs - from rRNA - from ocean PCR and metagenomic data
  • OPFs from metagenomic data
• James
  • OTUs filtered by narrower taxonomic range (e.g. families)
  • OTUs from both metagenomic and additional ocean PCR data
• Sam
  • Protein families
    • alignments, trees from metagenomic data for those families
  • Simulations
    • Generating and analyzing trees from simulated data
• Tom
  • All vs. all clustering of protein sequences from whole genome data
    • Build the families
• Dongying
  • Merge families from different phyla
    • MySQL database of relationships between taxonomy and sequences (map JGI <-> MicrobeDB?)
  • Install HMMER3 in centralized location
    • Get consensus sequences for HMM profiles to group HMMs/families into clusters
• Morgan
  • All vs. all BLASTs
  • Access to many metagenomic data sets with metadata (grab from CAMERA)?
• Steve
  • Alignments of metagenomic reads to more gene families (using AMPHORA?)
    • For GOS data set
    • Additional marker gene families from Dongying
    • Additional markers for different taxonomic groups (archaea, Actinos, etc.)