FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution

摘要: Motivation: Next generation sequencing technology generates highthroughput data, which allows us to detect fusion genes at both transcript and genomic levels. To genes, the current bioinformatics tools heavily rely on paired-end approaches overlook importance of reads that span junctions. Thus there is a need develop an efficient aligner events by accurate mapping these junction-spanning single reads, particularly when read gets longer with improvement in technology. Results: We present novel method, FusionMap, aligns directly genome without prior knowledge potential regions. FusionMap can single- datasets from either RNA-Seq or gDNA-Seq studies characterize junctions base-pair resolution. showed achieved high sensitivity specificity detection two simulated datasets, contained 75 nt reads. substantially higher than approach inner distance between pairs was small. Using K562 chronic myeloid leukemia cell line, we further demonstrated its accuracy single-end datasets. These combined results show provides systematic solution detecting through Availability: includes reference indexing, filtering, alignment reporting one package. The software free for noncommercial use (http://www.omicsoft.com/fusionmap).