Crossing the streams: a framework for streaming analysis of short DNA sequencing reads

5 We present a semi-streaming algorithm for k-mer spectral analysis of 6 DNA sequencing reads, together with a derivative approach that is fully 7 streaming. The approach can also be applied to genomic, transcriptomic, 8 and metagenomic data sets. We develop two tools for short-read analysis 9 based on these approaches, a method for semi-streaming k-mer-based error 10 trimming, and a method for the analysis of error profiles in short reads 11 using a streaming sublinear approach. These tools are implemented in the 12 khmer software package, which is freely available under the BSD License 13 at github.com/ged-lab/khmer/. 14