Rascaf: Improving Genome Assembly with RNA-seq Data

Low sequencing costs have recently made it possible for groups and even individual researchers to sequence the genome of the species they are studying. Two critical steps in every genome sequencing project are genome assembly and gene annotation. While abundant, short reads make assembly from next generation sequencing data difficult and lead to fragmented genomes, which in turn complicates gene annotation. To enhance both assembly and annotation, we propose to use the vast resources of RNA-seq data generated by each project to improve the completeness and contiguity of the assembled sequence. For this purpose, we developed Rascaf (RnA-seq SCAFfolder), a fast and efficient tool that leverages the long-range contiguity information from intron-spanning RNA-seq read pairs to detect new contig connections and improve the assembly, in particularly in the gene regions. When tested on both simulated and real data, the program was very accurate and found hundreds of new connections in the Rosaceae genomes. Rascaf is fast, has a small memory footprint and is easy-to-use, and can be readily incorporated into genome assembly projects to help improve the assembly and the gene annotations simultaneously. Funding: NSF IOS-1339134.