Summary: Tracking thousands of alternative splicing (AS) events genome-wide makes their downstream analysis computationally challenging and laborious. Here, we present Matt, the first UNIX command-line toolkit with focus on high-level AS analyses. With 50 commands it facilitates computational AS analyses by (i) expediting repetitive data-preparation tasks, (ii) offering routine high-level analyses, including the extraction of exon/intron features, discriminative feature detection, motif enrichment analysis, and the generation of motif RNA-maps, (iii) improving reproducibility by documenting all analysis steps and (iv) accelerating the implementation of own analysis pipelines by offering users to exploit its modular functionality. Availability and implementation: matt.crg.eu under GNU LGPLv3, together with comprehensive documentation and application examples. Matt is implemented in Perl and R, invokes pdfLATEX and depends only on Perl Core modules/the R Base package simplifying its installation.

This work was supported by the European Research Council [ERC-StG-LS2-637591 and ERC-AdG-MASCP-670146], the Spanish Ministry of Economy and Competitiveness [BFU2014-55076-P and BFU2014-55058-P], the EMBL partnership, and the CRG (SEV-2012-0208), Centro de Excelencia Severo Ochoa and CERCA programme.