  Background: Computational analysis of next-generation sequencing data is
outpaced by data generation in many cases. In one such case, paired-end reads
can be produced from the Illumina sequencing method faster than they can be
overlapped by downstream analysis. The advantages in read length and accuracy
provided by overlapping paired-end reads demonstrates the necessity for
software to efficiently solve this problem.
  Results: XORRO is an extremely efficient paired-end read overlapping program.
XORRO can overlap millions of short paired-end reads in a few minutes. It uses
64-bit registers with a two bit alphabet to represent sequences and does
comparisons using low-level logical operations like XOR, AND, bitshifting and
popcount.
  Conclusions: As of the writing of this manuscript, XORRO provides the fastest
solution to the paired-end read overlap problem. XORRO is available for
download at: sourceforge.net/projects/xorro-overlap/
