SPATA: A highly accurate GUI tool for de novo transcriptome assembly

Abstract

Transcript quantification using RNA-seq is central to contemporary and future transcriptomics research. The existing tools are useful but have much room for improvement. We present a new statistical model, a fast yet accurate transcript quantification algorithm. Our tool takes RNA-seq reads in fasta or fastq format as input and output transcript abundance through a few mouse clicks. Our method compares favorably with the existing GUI tools in terms of both time complexity and accuracy. Availability: Both simulation data used for method comparisons and the GUI tool are freely available at http://asammate.sourceforge.net/.

Tin Nguyen

Associate Professor