mTim: Rapid and accurate transcript reconstruction from RNA-Seq data

High-throughput sequencing technology applied to cellular mRNA (RNA-Seq) has revolutionized transcriptome studies [19, 17, 35, among many others]. In contrast to microarray platforms, which it has replaced in many applications, RNA-Seq can not only be used to accurately quantify known transcripts, but also to reveal the precise structure of transcripts at single-nucleotide resolution. RNA-Seq based transcript reconstruction has therefore become a valuable tool for the completion of genome annotations [22, 11, for instance] and further enabled subsequent analyses of differentially expressed genes [2], transcript isoforms [6, 4] and exons [3], all of which generally rely on correctly inferred transcript inventories. De novo transcript reconstruction is thus a pivotal step in the analysis of RNA-Seq data. There are two conceptually different strategies to approach this problem: one can either assemble transcripts directly from RNA-Seq reads using methodology that originated from genome assembly approaches [13, 23, 25].