====== Game Plan ======
Kevin outlined the steps we should take to evaluate the data we have now.  We currently have 454 contigs built with [[archive:bioinformatic_tools:gs_de_novo_assembler|Newbler]] (but with a high error rate, so likely repeat regions were being joined).  The 454 data has poor coverage as well, but may work well as a starting point for [[archive:bioinformatic_tools:price|PRICE]], using Illumina data to extend them.

So, our next steps are to:
  - Count kmers in Illumina data with [[archive:bioinformatic_tools:jellyfish|Jellyfish]]
  - Filter kmers with [[archive:bioinformatic_tools:quake|Quake]]
  - Trim with [[archive:bioinformatic_tools:seqprep|SeqPrep]]
  - Rebuild 454 contigs with [[archive:bioinformatic_tools:gs_de_novo_assembler|Newbler]] 2.5.3
  - Initialize PRICE with 454 contigs and extend with trimmed and filtered Illumina reads