Many exciting papers/preprints on RNAseq came out over the last few months. Among them, a recently posted preprint solves an important problem - improving annotations based on new RNAseq data. There were other papers on quantification, compression and search, and we like to cover them in the next few posts.
We present a new method, GRASS, for improving an initial annotation of de novo transcriptomes. GRASS makes the shared-sequence relationships between assembled contigs explicit in the form of a graph, and applies an algorithm that performs label propagation to transfer annotations between related contigs and modifies the graph topology iteratively. We demonstrate that GRASS increases the completeness and accuracy of the initial annotation, allows for improved differential analysis, and is very efficient, typically taking 10s of minutes.
Software Availability: GRASS is written in Python, and is freely-available under an open-source (BSD) license at https://github.com/COMBINE-lab/GRASS.