Introduction

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.

Publications

  1. Rascaf: Improving Genome Assembly with RNA Sequencing Data.
    Cite this
    Song L, Shankar DS, Florea L, 2016-11-01 - The plant genome

Credits

  1. Li Song
    Developer

  2. Dhruv S Shankar
    Developer

  3. Liliana Florea
    Investigator

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Summary
AccessionBT002976
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++, Perl
User InterfaceTerminal Command Line
Download Count0
Submitted ByLiliana Florea