Rascaf: Improving genome assembly with RNA sequencing data

Li Song, Dhruv S. Shankar, Liliana Florea

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


Abundant but short second-generation sequencing reads make assembly difficult, leading to fragmented genomes and gene annotations. Gene structure information from RNA sequences can be used to improve the completeness and contiguity of an assembly, but bioinformatics methods have been lacking. 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. It determines a heaviest path in an exon block graph that simultaneously represents a gene and the underlying contig relationships. Rascaf is more accurate than its competitors, highly precise, and finds thousands of new verifiable connections in several draft Rosaceae genomes. Lightweight and practical, it can be readily incorporated into sequencing pipelines to improve an assembly and its gene annotations.

Original languageEnglish (US)
JournalPlant Genome
Issue number3
StatePublished - Nov 2016

ASJC Scopus subject areas

  • Genetics
  • Agronomy and Crop Science
  • Plant Science


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