Molecular and Genetic Medicine

ISSN: 1747-0862

Open Access

Yi-Chen Huang

Institute of Information Science, Academia Sinica, Taipei, Taiwan

  • Research Article   
    Local Optimization for Chromosome-Level Assembly (LOCLA)
    Author(s): Wei-Hsuan Chuang*, Hsueh-Chien Cheng, Pao-Yin Fu, Yi-Chen Huang, Ping-Heng Hsieh, Shu-Hwa Chen, Pui-Yan Kwok, Chung-Yen Lin, Jan-Ming Ho and Yu-Jung Chang

    In this paper, we introduce a novel genome assembly optimization tool named LOCLA. It identifies reads aligned locally with high quality on gap flanks or scaffold boundaries, and assembles them into contigs for gap filling or scaffold connection. LOCLA enhances the quality of an assembly based on reads of diverse sequencing techniques, either 10x Genomics (10xG) Linked-Reads, PacBio HiFi reads or both. For example, with 10xG Linked-Reads, the long-range information provided by barcodes allows LOCLA to recruit additional reads belonging to the same gDNA molecule, resulting in accurate gap filling and increased sequence coverage. In our experiments, we started by creating a preliminary draft assembly for each dataset using assembly tools such as Supernova and Canu assembler based on the type of sequencing reads. The preliminary draft assembly could either be .. Read More»
    DOI: 10.37421/1747-0862.2023.17.613

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