Rascaf: Improving Genome Assembly with RNA Sequencing Data.Abundant but short second-generation sequencing reads make assembly difficult, leading to fragmented genomes and gene annotations.  Rascaf is a highly efficient tool leveraging long-range continuity information from intron spanning RNA sequencing (RNA-seq) read pairs to detect new contig connections.  Rascaf is more accurate than its competitors, highly precise, and finds thousands of new verifiable connections in several draft Rosaceae genomes. 
Rascaf
Rascaf: Improving Genome Assembly with RNA Sequencing Data.Abundant but short second-generation sequencing reads make assembly difficult, leading to fragmented genomes and gene annotations.  Rascaf is a highly efficient tool leveraging long-range continuity information from intron spanning RNA sequencing (RNA-seq) read pairs to detect new contig connections.  Rascaf is more accurate than its competitors, highly precise, and finds thousands of new verifiable connections in several draft Rosaceae genomes. 
Rascaf