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Popular sequence alignment tools such as BWA convert a reference genome to anindexing data structure based on the Burrows-Wheeler Transform (BWT), fromwhich matches to individual query sequences can be rapidly determined. Howeverthe utility of also indexing the query sequences themselves remains relativelyunexplored.  Here we show that an all-against-all comparison of two sequence collectionscan be computed from the BWT of each collection with the BWTs held entirely inexternal memory, i.e. on disk and not in RAM. As an application of thistechnique, we show that BWTs of transcriptomic and genomic reads can becompared to obtain reference-free predictions of splice junctions that havehigh overlap with results from more standard reference-based methods.  Code to construct and compare the BWT of large genomic data sets is availableat http://beetl.github.com/BEETL/ as part of the BEETL library.

Comparing DNA sequence collections by direct comparison of compressed text indexes