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The Plant Genome Abstract - Original Research

Rascaf: Improving Genome Assembly with RNA Sequencing Data


This article in TPG

  1. Vol. 9 No. 3
    unlockOPEN ACCESS
    Received: Mar 11, 2016
    Accepted: May 11, 2016
    Published: September 1, 2016

    * Corresponding author(s): florea@jhu.edu
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  1. Li Songa,
  2. Dhruv S. Shankarb and
  3. Liliana Florea *a
  1. a McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 1900 E Monument, Welch 113, Baltimore, MD 21205 and Dep. of Computer Science, Johns Hopkins Univ., 1900 E Monument, Welch 117, Baltimore, MD 21205
    b Dep. of Biomedical Engineering, Univ. of North Carolina, 333 S. Columbia St., Chapel Hill, NC 27514
Core Ideas:
  • Rascaf simultaneously improves an assembly and its gene annotations
  • Rascaf finds thousands of new contig connections in draft Fragaria genomes
  • Rascaf is a highly accurate, efficient, and practical tool for plant genome sequencing projects


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.

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