Lou, S.-K., Ni, B., Lo, L.-Y., Tsui, S. K.-W., Chan, T.-F., & Leung, K.-S. (2011). ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping. Bioinformatics (Oxford, England), 27(3), 421-2. doi: 10.1093/bioinformatics/btq656.
Summary: Sequencing reads generated by RNA-sequencing (RNA-seq) must first be mapped back to the genome through alignment before they can be further analyzed. Current fast and memory-saving short-read mappers could give us a quick view of the transcriptome. However, they are not designed for reads that span across splice junctions, nor for repetitive reads, which can be mapped to multiple locations in the genome (multi-reads). Here we describe a new software package: ABMapper, which is specifically designed for exploring all putative locations of reads that are mapped to splice junctions or repetitive in nature.
Availability and Implementation: The software is freely available at:http://abmapper.sourceforge.net/. The software is written in C++ and PERL. It runs on all major platforms and operating systems including Windows, Mac OS X and LINUX.