LRScaf

LRScaf (Long Reads Scaffolder) is a scalable and computationally efficient software tool to improve the contiguity of draft genome assemblies by utilizing long reads generated from third-generation sequencing (TGS) technologies. It aims to enhance the quality of fragmented assemblies initially constructed using next-generation sequencing (NGS) technologies.

In a comprehensive performance assessment, LRScaf demonstrated its ability to significantly boost assembly contiguity across various organisms, ranging from bacteria to large eukaryotic genomes. It outperformed other state-of-the-art scaffolders in terms of contiguity improvement, as measured by the NGA50 metric, on several organisms such as Arabidopsis thaliana, Solanum pennellii, Zea mays, and Homo sapiens.

Topic

Sequencing;Sequence assembly;Mapping;Plant biology

Detail

  • Operation: Genome assembly;De-novo assembly;Scaffolding

  • Software interface: Command-line interface

  • Language: Java

  • License: Not stated

  • Cost: Free of charge

  • Version name: 1.1.10

  • Credit: The Dapeng New District Special Fund for Industrial Development, the National Key Research and Development Program of China, the National Natural Science Foundation of China, the Fundamental Research Funds for Central Non-profit Scientific Institution, the Fund of Key Laboratory of Shenzhen, the Agricultural Science and Technology Innovation Program, the Shenzhen Science and Technology Research Funding, the Key Forestry Public Welfare Project, the Agricultural Science and Technology Innovation Program Cooperation and Innovation Mission.

  • Input: -

  • Output: -

  • Contact: Jue Ruan ruanjue@caas.cn

  • Collection: -

  • Maturity: -

Publications

  • LRScaf: improving draft genomes using long noisy reads.
  • Qin M, et al. LRScaf: improving draft genomes using long noisy reads. LRScaf: improving draft genomes using long noisy reads. 2019; 20:955. doi: 10.1186/s12864-019-6337-2
  • https://doi.org/10.1186/S12864-019-6337-2
  • PMID: 31818249
  • PMC: PMC6902338

Download and documentation

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