Published in

Oxford University Press (OUP), Bioinformatics, 3(27), p. 421-422

DOI: 10.1093/bioinformatics/btq656

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ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping

Journal article published in 2010 by Shao-Ke Lou, Bing Ni, Leung-Yau Lo, Stephen Kwok-Wing Tsui, Ting-Fung Chan ORCID, Kwong-Sak Leung
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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 neither 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.