Fusion events identified through the Trans-ABySS pipeline:  Reads are
assembled into contigs using ABySS at multiple k-mer lengths.  The
multi-k assemblies are then merged into a single meta-assembly where
perfectly matching sub-sequences are removed.  The merged contig set is
aligned against the reference genomic sequence using BLAT or BWA-SW (for
genomic libraries).  Split alignments are captured as putative 'fusion'
events and filtered by criteria such as the two alignments must capture
at least 90% of the contig length, the 2 query regions cannot overlap
more than 5% of the contig length, etc (for more information please refer 
to the user manual at http://www.bcgsc.ca/downloads/trans-abyss/data/trans-abyss-manual-v1.3.2.pdf). 
The fusion events are then checked for read support based on 1) discordant read-pairs using a
reads-to-genome BAM file generated by BCGSC's WTSS pipeline (using BWA);
and 2) junction-spanning reads using a  reads-to-contigs BAM file
generated by BWA.  Events that have at least 4 discordant read-pairs and
2 spanning reads are kept.