Game Plan

Kevin outlined the steps we should take to evaluate the data we have now. We currently have 454 contigs built with 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 PRICE, using Illumina data to extend them.

So, our next steps are to:

1. Count kmers in Illumina data with Jellyfish
2. Filter kmers with Quake
3. Trim with SeqPrep
4. Rebuild 454 contigs with Newbler 2.5.3
5. Initialize PRICE with 454 contigs and extend with trimmed and filtered Illumina reads