A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms

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Abstract

Background: With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from high-throughput sequencing data, they are very memory-intensive, limiting their applications to small data sets with few libraries. Results: We develop a transcriptome assembly algorithm that recovers alternatively spliced isoforms and expression levels while utilizing as many RNA-Seq libraries as possible that contain hundreds of gigabases of data. New techniques are developed so that computations can be performed on a computing cluster with moderate amount of physical memory. Conclusions: Our strategy minimizes memory consumption while simultaneously obtaining comparable or improved accuracy over existing algorithms. It provides support for incremental updates of assemblies when new libraries become available.

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Sze, S. H., Pimsler, M. L., Tomberlin, J. K., Jones, C. D., & Tarone, A. M. (2017). A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms. BMC Genomics, 18. https://doi.org/10.1186/s12864-017-3735-1

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