SOAPdenovo-Trans: de novo transcriptome assembly with short…

Abstract

Transcriptome sequencing has long been the favored method for quickly and inexpensively obtaining a large number of gene sequences from an organism with no reference genome. Owing to the rapid increase in throughputs and decrease in costs of next- generation sequencing, RNA-Seq in particular has become the method of choice. However, the very short reads (e.g. 2 × 90 bp paired ends) from next generation sequencing makes de novo assembly to recover complete or full-length transcript sequences an algorithmic challenge. Here, we present SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse. Using as our benchmarks the known transcripts from these well-annotated genomes (sequenced a decade ago), we assessed how SOAPdenovo-Trans and two other popular transcriptome assemblers handled such practical issues as alternative splicing and variable expression levels. Our conclusion is that SOAPdenovo-Trans provides higher contiguity, lower redundancy and faster execution. Source code and user manual are available at http://sourceforge.net/projects/soapdenovotrans/.

MeSH Terms

Algorithms Alternative Splicing Animals Gene Expression Profiling/methods Genomics/methods High-Throughput Nucleotide Sequencing/methods Mice Oryza/genetics Sequence Analysis, RNA/methods

Authors & Affiliations

16 authors, click to expand affiliations / ORCID

Xie Yinlong

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi ArabiaSchool of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawha

Wu Gengxiong

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.

Tang Jingbo

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi ArabiaSchool of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawha

Luo Ruibang

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi ArabiaSchool of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawha

Patterson Jordan

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.

Liu Shanlin

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.

Huang Weihua

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.

He Guangzhu

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.

Gu Shengchang

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi ArabiaSchool of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawha

Li Shengkang

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.

Zhou Xin

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.

Lam Tak-Wah

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.

Li Yingrui

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.

Xu Xun

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi Arabia.

Wong Gane Ka-Shu

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi ArabiaSchool of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawha

Wang Jun

School of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21589, Saudi ArabiaSchool of Bioscience and Bioengineering, South China University of Technology 510006, Guangzhou, China, BGI-Shenzhen, Shenzhen 518083, China, HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory and Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, Institute of Biomedical Engineering, XiangYa School of Medicine, Central South University, Changsha 410008, China, BGI-tech, BGI-Shenzhen, Shenzhen 518083, China, Department of Medicine, University of Alberta, Edmonton, AB T6G 2E1, Canada, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada, The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen DK-2200, Denmark, Department of Biology, University of Copenhagen, Copenhagen DK-2200, Denmark and Princess Al Jawha

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.

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