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  • We propose a novel method and software tool, Strawberry, for transcript reconstruction and quantification from RNA-Seq data under the guidance of genome alignment and independent of gene annotation. Availability: Strawberry is written in C++14, and is available as open source software at https://github.com/ruolin/strawberry under the MIT license. Strawberry was written in C++14 and utilizes features such as threading library for parallelization. Strawberry is available as a free software at https://github.com/ruolin/strawberry under the MIT license. This paper introduced Strawberry, a fast, accurate genome-guide assembler and quantification tool for RNA-Seq data.
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