Illumina Data Reduction Primer

Here are some notes on how I analyze Illumina data. I would appreciate any comments on how to improve, supplement or extend these methods.

I’m currently using an Amazon Machine Image to analyze PacBio data, and hope to write about this experience soon. Suffice it to say that the high error rate and variable read lengths make the process much more challenging than was the case for Illumina paired reads.

-- Eric Kofoid

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