X-MATE: A flexible system for mapping short read data

A crucial step in the analysis of deep sequencing data is mapping to a reference genome. Accurate and complete mapping greatly enhances the potential discovery of biological results and improves statistical predictions while inaccurate or incomplete mapping may lead to noise and reduced coverage.

We recently presented RNA-MATE, a pipeline for the recursive mapping of RNASeq data sets. With the rapid increase in genome resequencing projects, progression of available mapping software and the evolution of file formats, we present X-MATE, an updated version of RNA-MATE, capable of mapping both RNASeq and DNA data sets and with improved performance, output file formats, configuration files, and flexibility in core mapping software.

X-MATE is available at: http://grimmond.imb.uq.edu.au/X-MATE/