Thanks to reader Heng Li, we came to know about a number of very good papers on sequence comparison from Anthony J. Cox and his colleagues.
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the BurrowsWheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the utility of also indexing the query sequences themselves remains relatively unexplored. Here we show that an all-against-all comparison of two sequence collections can be computed from the BWT of each collection with the BWTs held entirely in external memory, i.e. on disk and not in RAM. As an application of this technique, we show that BWTs of transcriptomic and genomic reads can be compared to obtain reference-free predictions of splice junctions that have high overlap with results from more standard reference-based methods. Code to construct and compare the BWT of large genomic data sets is available at http://beetl.github.com/BEETL/ as part of the BEETL library.
You know what is crazy? The first paper is freely available from arxiv, but Springer charges $30 minus 5 cents to let you see it from their website ! $30 for merely posting intellectual work by others on a website, when you do not have to pay the intellectual contributors anything???
Oh, that is not all. There will be VAT on top of that, because government thinks you derive the same pleasure by ‘consuming’ a BWT paper as others do by flipping through Playboy magazine.
What a broken system !