SHE-RA SHortread Error-Reducing Aligner

Constructing composite sequences from overlapping mate-reads. In order to align overlapping mate reads and produce accurate composite fragments, we developed the SHERA pacakge, a set of perl modules and scripts. The algorithm was designed to be broadly applicable to mated reads, independent of the sequencing technology. The source code is freely available at http://almlab.mit.edu/ALM/Software/Software.html. In brief, SHERA takes overlapping short reads as input, finds the best alignment, produces a composite read, calculates new quality scores for the overlapping bases, and scores the alignment confidence. A detailed description of each of these steps is provided below. We also describe our procedure for evaluating false alignment rates on both real and simulated reads.