The JAFFA pipeline. An example of the JAFFA pipeline is demonstrated in detail using the RPS6KB1-VMP1 fusion from the MCF-7 breast cancer cell line dataset. Step 1: RNA-Seq reads are first filtered to remove intronic and intergenic reads. 50 bp reads would then be assembled into contigs using Oases. For longer reads, this step is not necessary. Step 2: The resulting tumour sequences are then aligned to the reference transcriptome and those that align to multiple genes are selected. These contigs make up a set of initial candidate fusions. Step 3: Next, the pipeline counts the number of reads and read pairs that span the breakpoint. Step 4: Candidates are then aligned to the human genome. Genomic coordinates of the breakpoint are determined. Step 5: Further selection and candidate classification is carried out using quantities such as genomic gap size, supporting reads and alignment of breakpoints to exon-exon boundaries. Step 6: A final list of candidates is reported along with their sequence.