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====== Game Plan ====== Kevin outlined the steps we should take to evaluate the data we have now. We currently have 454 contigs built with [[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 [[bioinformatic_tools:price|PRICE]], using Illumina data to extend them. So, our next steps are to: - Count kmers in Illumina data with [[bioinformatic_tools:jellyfish|Jellyfish]] - Filter kmers with [[bioinformatic_tools:quake|Quake]] - Trim with [[bioinformatic_tools:seqprep|SeqPrep]] - Rebuild 454 contigs with [[bioinformatic_tools:gs_de_novo_assembler|Newbler]] 2.5.3 - Initialize PRICE with 454 contigs and extend with trimmed and filtered Illumina reads
