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A Divide-and-Conquer Algorithm for Large-scale de Novo Transcriptome Assembly Through Combining Small Assemblies From Existing Algorithms

NCJ Number
253425
Date Published
2018
Length
8 pages
Author(s)
Sing-Hoi Sze; Jonathan J. Parrott; Aarib M. Tarone
Agencies
NIJ-Sponsored
Publication Type
Research (Applied/Empirical), Report (Study/Research), Report (Grant Sponsored), Program/Project Description
Grant Number(s)
2012-DN-BX-K024, 2015-DN-BX-K020
Annotation
This project developed a divide-and-conquer strategy that enables algorithms that can assemble a large amount of RNA-Seq data to be utilized by subdividing a large RNA-Seq data set into small libraries.
Abstract
Although the continued development of high-throughput sequencing has facilitated studies of entire transcriptomes in non-model organisms, the incorporation of an increasing amount of RNA-Seq libraries has made de novo transcriptome assembly difficult. Although algorithms that can assemble a large amount of RNA-Seq data are available, they are generally very memory-intensive and can only be used to construct small assemblies. In the proposed data set with small libraries, each individual library is assembled independently by an existing algorithm, and a merging algorithm is developed to combine these assemblies by picking a subset of high-quality transcripts to form a large transcriptome. When compared to existing algorithms that return a single assembly directly, this strategy achieves comparable or increased accuracy as memory-efficient algorithms that can be used to process a large amount of RNA-Seq data, and comparable or decreased accuracy as memory-intensive algorithms that can only be used to construct small assemblies. This divide-and-conquer strategy enables memory-intensive de novo transcriptome assembly algorithms to be utilized to construct large assemblies. (publisher abstract modified)
Date Created: July 20, 2021